NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1391895249|ref|NP_001350619|]
View 

5' exonuclease Apollo isoform c [Homo sapiens]

Protein Classification

DNA cross-link repair protein( domain architecture ID 10888586)

DNA cross-link repair protein similar to Arabidopsis thaliana SNM1, which is involved in the repair of DNA lesions formed by oxidative stress

Gene Ontology:  GO:0006974|GO:0005634
PubMed:  12177301|20528238|26582912

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 6-151 2.87e-56

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


:

Pssm-ID: 293831  Cd Length: 160  Bit Score: 182.74  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   6 IPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTW-ARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPlde 84
Cdd:cd16273    19 IPGTSFVVDAFKYGKIPGISAYFLSHFHSDHYGGLTKSWsHGPIYCSEITANLVKLKLKVDEEYIVVLPMNTPVEID--- 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391895249  85 igqETMTVTLLDANHCPGSVMFLFEGYFG-TILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNP 151
Cdd:cd16273    96 ---GDVSVTLLDANHCPGAVMFLFELPDGrRILHTGDFRANPEMLEHPLLLGKRRIDTVYLDTTYCNP 160
DRMBL super family cl06523
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 216-299 1.41e-12

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


The actual alignment was detected with superfamily member pfam07522:

Pssm-ID: 429512  Cd Length: 108  Bit Score: 63.83  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249 216 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 275
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 1391895249 276 HSSYSELRAFVAALKPCQVVPIVS 299
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
 
Name Accession Description Interval E-value
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 6-151 2.87e-56

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293831  Cd Length: 160  Bit Score: 182.74  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   6 IPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTW-ARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPlde 84
Cdd:cd16273    19 IPGTSFVVDAFKYGKIPGISAYFLSHFHSDHYGGLTKSWsHGPIYCSEITANLVKLKLKVDEEYIVVLPMNTPVEID--- 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391895249  85 igqETMTVTLLDANHCPGSVMFLFEGYFG-TILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNP 151
Cdd:cd16273    96 ---GDVSVTLLDANHCPGAVMFLFELPDGrRILHTGDFRANPEMLEHPLLLGKRRIDTVYLDTTYCNP 160
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 216-299 1.41e-12

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 63.83  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249 216 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 275
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 1391895249 276 HSSYSELRAFVAALKPCQVVPIVS 299
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
28-129 4.25e-09

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 56.74  E-value: 4.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGL-----SSTWAR-----PLYCSPITAHLLHRHLQVSKQW----IQALEVGESHVLPLDEIgqetmTVT 93
Cdd:COG1234    57 FITHLHGDHIAGLpgllsTRSLAGrekplTIYGPPGTKEFLEALLKASGTDldfpLEFHEIEPGEVFEIGGF-----TVT 131

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1391895249  94 LLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLK 129
Cdd:COG1234   132 AFPLDHPVPAYGYRFEEPGRSLVYSGDTRPCEALVE 167
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 17-128 7.49e-07

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 49.09  E-value: 7.49e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   17 SLRRAGTARL--FFLSHMHSDHTVG---LSSTWARPLYCSPITAHLLhRHLQVSKQWIQALEVGESHVLPLDE-----IG 86
Cdd:smart00849  27 ELKKLGPKKIdaIILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELL-KDLLALLGELGAEAEPAPPDRTLKDgdeldLG 105

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1391895249   87 QETMTVTLLdANHCPGSVMFLFEGyfGTILYTGDFRYTPSML 128
Cdd:smart00849 106 GGELEVIHT-PGHTPGSIVLYLPE--GKILFTGDLLFAGGDG 144
Lactamase_B_2 pfam12706
Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and ...
 28-130 5.34e-06

Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and is related to pfam00753.


Pssm-ID: 432732 [Multi-domain]  Cd Length: 196  Bit Score: 46.92  E-value: 5.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSS---TWARPLYCSPITAhllhRHLqvsKQWIQALEVGES-----HVLPLDE---IGQETMTVTLLD 96
Cdd:pfam12706  33 LLTHDHYDHLAGLLDlreGRPRPLYAPLGVL----AHL---RRNFPYLFLLEHygvrvHEIDWGEsftVGDGGLTVTATP 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1391895249  97 ANH--------CPGSVM-FLFEGYFGTILYTGDFRYTPSMLKE 130
Cdd:pfam12706 106 ARHgsprgldpNPGDTLgFRIEGPGKRVYYAGDTGYFPDEIGE 148
 
Name Accession Description Interval E-value
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 6-151 2.87e-56

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293831  Cd Length: 160  Bit Score: 182.74  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   6 IPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTW-ARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPlde 84
Cdd:cd16273    19 IPGTSFVVDAFKYGKIPGISAYFLSHFHSDHYGGLTKSWsHGPIYCSEITANLVKLKLKVDEEYIVVLPMNTPVEID--- 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391895249  85 igqETMTVTLLDANHCPGSVMFLFEGYFG-TILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNP 151
Cdd:cd16273    96 ---GDVSVTLLDANHCPGAVMFLFELPDGrRILHTGDFRANPEMLEHPLLLGKRRIDTVYLDTTYCNP 160
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 6-151 1.84e-38

5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) which is a 5'-exonuclease and functions in interstrand cross-links (ICL) repair. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293856 [Multi-domain]  Cd Length: 157  Bit Score: 136.11  E-value: 1.84e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   6 IPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLHRHLQVSKQWIqalevgesHVLPLD-E 84
Cdd:cd16298    19 IPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQYI--------NVLPMNtE 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391895249  85 IGQETMTVTLLDANHCPGSVMFLFEGYFGT-ILYTGDFRYTPSMLKEPALtLGKQIHTLYLDNTNCNP 151
Cdd:cd16298    91 CIVNGVKVVLLDANHCPGAVMILFRLPSGTlVLHTGDFRADPSMERYPEL-IGQKIHTLYLDTTYCSP 157
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
 24-151 5.58e-26

artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Inactivation of Artemis causes severe combined immunodeficiency (SCID). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293855  Cd Length: 171  Bit Score: 103.36  E-value: 5.58e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  24 ARLFFLSHMHSDHTVGLSSTWARP---------LYCSPITAHLLHRHLQVS--KQWIQALEVGESHVLPL-DEIG--QET 89
Cdd:cd16297    26 ARAYFLSHCHKDHMKGLRAPGLKRrlkaslkvkLYCSPVTKELLLTNPKYAfwENHIVSLEIDTPTQISLvDEATgeKED 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1391895249  90 MTVTLLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLKEPAL----TLGKQIHTLYLDNTNCNP 151
Cdd:cd16297   106 VVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAVGEAARMELlhsgDRVKDIQSVYLDTTFCDP 171
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 216-299 1.41e-12

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 63.83  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249 216 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 275
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 1391895249 276 HSSYSELRAFVAALKPCQVVPIVS 299
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
metallo-hydrolase-like_MBL-fold cd07732
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 28-122 8.52e-10

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain; Includes functionally uncharacterized Enterococcus faecalis EF2904. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry.


Pssm-ID: 293818 [Multi-domain]  Cd Length: 202  Bit Score: 58.01  E-value: 8.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTvGLSSTWAR--PLYCSPITAHLLHRHLQVSK------QWIQALEVGESHvlpldEIGQETMTVTLLDanH 99
Cdd:cd07732    80 LLSHAHLDHY-GLLNYLRPdiPVYMGEATKRILKALLPFFGegdpvpRNIRVFESGKSF-----TIGDFTVTPYLVD--H 151

                          90       100
                  ....*....|....*....|....
gi 1391895249 100 -CPGSVMFLFEGYFGTILYTGDFR 122
Cdd:cd07732   152 sAPGAYAFLIEAPGKRIFYTGDFR 175
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
28-129 4.25e-09

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 56.74  E-value: 4.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGL-----SSTWAR-----PLYCSPITAHLLHRHLQVSKQW----IQALEVGESHVLPLDEIgqetmTVT 93
Cdd:COG1234    57 FITHLHGDHIAGLpgllsTRSLAGrekplTIYGPPGTKEFLEALLKASGTDldfpLEFHEIEPGEVFEIGGF-----TVT 131

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1391895249  94 LLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLK 129
Cdd:COG1234   132 AFPLDHPVPAYGYRFEEPGRSLVYSGDTRPCEALVE 167
TTHA0252-CPSF-like_MBL-fold cd16295
Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; ...
 28-133 1.74e-07

Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; Includes the archaeal cleavage and polyadenylation specificity factors (CPSFs) such as Methanothermobacter thermautotrophicus MTH1203, and Pyrococcus horikoshii PH1404. In addition to the MBL-fold metallo-hydrolase nuclease and the beta-CASP domains, members of this subgroup contain two contiguous KH domains. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293853 [Multi-domain]  Cd Length: 197  Bit Score: 51.31  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGL----SSTWARPLYCSPITAHLLHRHLQVS-KqwIQALEVGESHVLPLD---------------EIGQ 87
Cdd:cd16295    56 ILTHAHLDHSGRLpllvKEGFRGPIYATPATKDLAELLLLDSaK--IQEEEAEHPPAEPLYteedvekalkhfrpvEYGE 133

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1391895249  88 ET-----MTVTLLDANHCPGSVMFLFEGYFG-TILYTGDFRYTPS-MLKEPAL 133
Cdd:cd16295   134 PFeigpgVKVTFYDAGHILGSASVELEIGGGkRILFSGDLGRKNTpLLRDPAP 186
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 17-128 7.49e-07

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 49.09  E-value: 7.49e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249   17 SLRRAGTARL--FFLSHMHSDHTVG---LSSTWARPLYCSPITAHLLhRHLQVSKQWIQALEVGESHVLPLDE-----IG 86
Cdd:smart00849  27 ELKKLGPKKIdaIILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELL-KDLLALLGELGAEAEPAPPDRTLKDgdeldLG 105

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1391895249   87 QETMTVTLLdANHCPGSVMFLFEGyfGTILYTGDFRYTPSML 128
Cdd:smart00849 106 GGELEVIHT-PGHTPGSIVLYLPE--GKILFTGDLLFAGGDG 144
metallo-hydrolase-like_MBL-fold cd06262
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 28-121 8.32e-07

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


Pssm-ID: 293792 [Multi-domain]  Cd Length: 188  Bit Score: 49.21  E-value: 8.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVG---LSSTWARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPL---DEIGQETMTVTLLDA-NHC 100
Cdd:cd06262    50 LLTHGHFDHIGGlaeLKEAPGAPVYIHEADAELLEDPELNLAFFGGGPLPPPEPDILLedgDTIELGGLELEVIHTpGHT 129

                          90       100
                  ....*....|....*....|.
gi 1391895249 101 PGSVMFLFEGyfGTILYTGDF 121
Cdd:cd06262   130 PGSVCFYIEE--EGVLFTGDT 148
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 19-132 1.88e-06

Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; CPSF3 (cleavage and polyadenylation specificity factor subunit 3; also known as cleavage and polyadenylation specificity factor 73 kDa subunit, CPSF-73) and CPSF2 (also known as cleavage and polyadenylation specificity factor 100 kDa subunit /CPSF-100) are components of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. CPSF3 functions as a 3' endonuclease. Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)), and Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74) are subunits of Integrator, a metazoan-specific multifunctional protein complex composed of 14 subunits. Integrator has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293820 [Multi-domain]  Cd Length: 193  Bit Score: 48.10  E-value: 1.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  19 RRAGTARLFFLSHMHSDHTVGLS-----STWARPLYCSPITAHLL-------HRHLQVSKQW-----IQALEVGESHVLP 81
Cdd:cd07734    45 LLPPEIDAILISHFHLDHCGALPylfrgFIFRGPIYATHPTVALGrllledyVKSAERIGQDqslytPEDIEEALKHIVP 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1391895249  82 LD-----EIGQEtMTVTLLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLKEPA 132
Cdd:cd07734   125 LGygqsiDLFPA-LSLTAYNAGHVLGAAMWEIQIYGEKLVYTGDFSNTEDRLLPAA 179
Lactamase_B_2 pfam12706
Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and ...
 28-130 5.34e-06

Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and is related to pfam00753.


Pssm-ID: 432732 [Multi-domain]  Cd Length: 196  Bit Score: 46.92  E-value: 5.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSS---TWARPLYCSPITAhllhRHLqvsKQWIQALEVGES-----HVLPLDE---IGQETMTVTLLD 96
Cdd:pfam12706  33 LLTHDHYDHLAGLLDlreGRPRPLYAPLGVL----AHL---RRNFPYLFLLEHygvrvHEIDWGEsftVGDGGLTVTATP 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1391895249  97 ANH--------CPGSVM-FLFEGYFGTILYTGDFRYTPSMLKE 130
Cdd:pfam12706 106 ARHgsprgldpNPGDTLgFRIEGPGKRVYYAGDTGYFPDEIGE 148
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 28-186 5.82e-06

RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 48.26  E-value: 5.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSSTWAR----PLYCSPITAHLLHR------HLQVSK----------------QWIQALEVGESHVLP 81
Cdd:COG1236    55 VLTHAHLDHSGALPLLVKEgfrgPIYATPATADLARIllgdsaKIQEEEaeaeplyteedaeralELFQTVDYGEPFEIG 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  82 ldeigqeTMTVTLLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLKEPAlTLGKQIHTLYLDNTNCNPalVLPSRQEA 161
Cdd:COG1236   135 -------GVRVTFHPAGHILGSAQVELEVGGKRIVFSGDYGREDDPLLAPP-EPVPPADVLITESTYGDR--LHPPREEV 204

                         170       180
                  ....*....|....*....|....*..
gi 1391895249 162 AHQIVQLIRK--HPQHNIKIGLYSLGK 186
Cdd:COG1236   205 EAELAEWVREtlARGGTVLIPAFALGR 231
RnjA COG0595
mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];
28-125 1.77e-05

mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440360 [Multi-domain]  Cd Length: 553  Bit Score: 46.98  E-value: 1.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSSTWAR---PLYCSPITAHLLHRHLQ----VSKQWIQALEVGESHvlpldEIGQetMTVTLLDANH- 99
Cdd:COG0595    68 VLTHGHEDHIGALPYLLKElnvPVYGTPLTLALLEAKLKehglLKKVKLHVVKPGDRI-----KFGP--FKVEFFRVTHs 140

                          90       100
                  ....*....|....*....|....*...
gi 1391895249 100 CPGSVMFLFEGYFGTILYTGDFR--YTP 125
Cdd:COG0595   141 IPDSLGLAIRTPAGTIVHTGDFKfdQTP 168
class_II_PDE_MBL-fold cd07735
class II cyclic nucleotide phosphodiesterases Saccharomyces cerevisiae PDE1, Dictyostelium ...
 27-120 2.14e-05

class II cyclic nucleotide phosphodiesterases Saccharomyces cerevisiae PDE1, Dictyostelium discoideum PDE1 and PDE7, and related proteins; MBL-fold metallo-hydrolase domain; Cyclic nucleotide phosphodiesterases (PDEs) decompose the second messengers cyclic adenosine and guanosine 3',5'-monophosphate (cAMP and cGMP, respectively). Saccharomyces cerevisiae PDE1 and Dictyostelium discoideum PDE1 and PDE7, have dual cAMP/cGMP specificity. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293821  Cd Length: 259  Bit Score: 45.67  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  27 FFLSHMHSDHTVGL---------SSTWARPLYCSPITAHLLHRHL---QVskqW--IQALEVGESHVLPLDEIGQET--- 89
Cdd:cd07735    69 YLITHAHLDHIAGLpllspndggQRGSPKTIYGLPETIDALKKHIfnwVI---WpdFTSIPSGKYPYLRLEPIEPEYpia 145

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1391895249  90 ---MTVTLLDANH-CPGSVMFLFEGYFGTILYTGD 120
Cdd:cd07735   146 ltgLSVTAFPVSHgVPVSTAFLIRDGGDSFLFFGD 180
RNaseJ_MBL-fold cd07714
RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a ...
 28-125 2.28e-05

RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a prokaryotic ribonuclease which plays a key part in RNA processing and in RNA degradation. It can act as an endonuclease which is specific for single-stranded regions of RNA irrespective of their sequence or location, and as a processive 5' exonuclease which only acts on substrates having a single phosphate or a hydroxyl at the 5' end. Many bacterial species have only one RNase J, but some, such as Bacillus subtilis, have two. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293800 [Multi-domain]  Cd Length: 248  Bit Score: 45.48  E-value: 2.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSSTWAR---PLYCSPITAHLLHRHLQ----VSKQWIQALEVGESHvlpldEIGQetMTVTLLDANHC 100
Cdd:cd07714    60 FITHGHEDHIGALPYLLPElnvPIYATPLTLALIKKKLEefklIKKVKLNEIKPGERI-----KLGD--FEVEFFRVTHS 132

                          90       100
                  ....*....|....*....|....*...
gi 1391895249 101 -PGSVMFLFEGYFGTILYTGDFR--YTP 125
Cdd:cd07714   133 iPDSVGLAIKTPEGTIVHTGDFKfdQTP 160
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 28-172 7.20e-05

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 44.12  E-value: 7.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLsSTWAR-------PLYCSPITAHLLHRHL-QVSKQWIQALEVgesHVLPLDE---IGQetMTVTLLD 96
Cdd:COG1235    73 LLTHEHADHIAGL-DDLRPrygpnpiPVYATPGTLEALERRFpYLFAPYPGKLEF---HEIEPGEpfeIGG--LTVTPFP 146

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1391895249  97 ANH-CPGSVMFLFEGYFGTILYTGDFRYTPSMLKEpALtlgKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKH 172
Cdd:COG1235   147 VPHdAGDPVGYRIEDGGKKLAYATDTGYIPEEVLE-LL---RGADLLILDATYDDPEPGHLSNEEALELLARLGPKR 219
TTHA1623-like_MBL-fold cd16322
uncharacterized Thermus thermophilus TTHA1623 and related proteins; MBL-fold metallo hydrolase ...
 29-120 7.75e-05

uncharacterized Thermus thermophilus TTHA1623 and related proteins; MBL-fold metallo hydrolase domain; Includes the MBL-fold metallo hydrolase domain of uncharacterized Thermus thermophilus TTHA1623 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. This family includes homologs present in a wide range of bacteria and archaea and some eukaryota. Members of the MBL-fold metallo-hydrolase superfamily exhibit a variety of active site metallo-chemistry, TTHA1623 exhibiting a uniquely shaped putative substrate-binding pocket with a glyoxalase II-type metal-coordination mode.


Pssm-ID: 293877 [Multi-domain]  Cd Length: 204  Bit Score: 43.49  E-value: 7.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  29 LSHMHSDHTVGLSSTWAR---PLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPLDEigQETMTVTLLD------ANH 99
Cdd:cd16322    52 LTHAHFDHVGGVADLRRHpgaPVYLHPDDLPLYEAADLGAKAFGLGIEPLPPPDRLLED--GQTLTLGGLEfkvlhtPGH 129

                          90       100
                  ....*....|....*....|.
gi 1391895249 100 CPGSVMFLFEGyfGTILYTGD 120
Cdd:cd16322   130 SPGHVCFYVEE--EGLLFSGD 148
Lactamase_B pfam00753
Metallo-beta-lactamase superfamily;
28-157 1.45e-04

Metallo-beta-lactamase superfamily;


Pssm-ID: 425851 [Multi-domain]  Cd Length: 196  Bit Score: 42.74  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGL----SSTWARPLYCSPITAHLLHRHLQVS---KQWIQALEVGESHVLPLDEIGQETMTVTLLDANHC 100
Cdd:pfam00753  48 ILTHGHFDHIGGLgelaEATDVPVIVVAEEARELLDEELGLAasrLGLPGPPVVPLPPDVVLEEGDGILGGGLGLLVTHG 127

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391895249 101 PG--SVMFLFEGYFGTILYTGDFRYTPSMLKEP-----ALTLGKQIHTLYLDN----TNCNPALVLPS 157
Cdd:pfam00753 128 PGhgPGHVVVYYGGGKVLFTGDLLFAGEIGRLDlplggLLVLHPSSAESSLESllklAKLKAAVIVPG 195
RNaseZ_MBL-fold cd16272
Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as ...
 28-126 1.88e-04

Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. It includes the C-terminus of human ELAC2 and Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293830 [Multi-domain]  Cd Length: 180  Bit Score: 41.87  E-value: 1.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHTVGLSST-WAR---------PLYCSPITAHLLHRHLQVsKQWIQALEvGESHVLPLDEIGQETM----TVT 93
Cdd:cd16272    55 FLSHFHLDHIGGLPTLlFARryggrkkplTIYGPKGIKEFLEKLLNF-PVEILPLG-FPLEIEELEEGGEVLElgdlKVE 132

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1391895249  94 LLDANHCPGSVMFLFEgYFG-TILYTGDFRYTPS 126
Cdd:cd16272   133 AFPVKHSVESLGYRIE-AEGkSIVYSGDTGPCEN 165
GloB COG0491
Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General ...
 28-120 2.77e-03

Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General function prediction only];


Pssm-ID: 440257 [Multi-domain]  Cd Length: 215  Bit Score: 38.90  E-value: 2.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDHtVGLSSTWAR----PLYCSPITAHLLHRhlQVSKQWIQALEVGESHVLPLD---EIGQETMTVTLLDAnHC 100
Cdd:COG0491    56 LLTHLHPDH-VGGLAALAEafgaPVYAHAAEAEALEA--PAAGALFGREPVPPDRTLEDGdtlELGGPGLEVIHTPG-HT 131

                          90       100
                  ....*....|....*....|
gi 1391895249 101 PGSVMFLFEGyfGTILYTGD 120
Cdd:COG0491   132 PGHVSFYVPD--EKVLFTGD 149
UlaG COG2220
L-ascorbate lactonase UlaG, metallo-beta-lactamase superfamily [Carbohydrate transport and ...
 28-127 8.65e-03

L-ascorbate lactonase UlaG, metallo-beta-lactamase superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 441822 [Multi-domain]  Cd Length: 224  Bit Score: 37.59  E-value: 8.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391895249  28 FLSHMHSDH-----TVGLSSTWArPLYCSPITAHLLHRHlQVSKqwIQALEVGESHVLpldeigqETMTVTLLDANHCPG 102
Cdd:COG2220    53 LVTHDHYDHlddatLRALKRTGA-TVVAPLGVAAWLRAW-GFPR--VTELDWGESVEL-------GGLTVTAVPARHSSG 121

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1391895249 103 --------SVMFLFEGYFGTILYTGDFRYTPSM 127
Cdd:COG2220   122 rpdrngglWVGFVIETDGKTIYHAGDTGYFPEM 154
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH