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Conserved domains on  [gi|20978506|sp|Q9BXS1|]
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RecName: Full=Isopentenyl-diphosphate delta-isomerase 2; AltName: Full=Isopentenyl pyrophosphate isomerase 2; Short=IPP isomerase 2; Short=IPPI2

Protein Classification

NUDIX domain-containing protein( domain architecture ID 225)

NUDIX domain-containing protein may catalyze the hydrolysis of nucleoside diphosphates linked to other moieties (X); it would require a divalent cation, such as Mg2+ or Mn2+ for its activity

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUDIX_Hydrolase super family cl00447
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 6-227 2.06e-79

NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


The actual alignment was detected with superfamily member PLN02552:

Pssm-ID: 469772 [Multi-domain]  Cd Length: 247  Bit Score: 238.09  E-value: 2.06e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    6 LDWVDRRQLQRLEemLIVVDENDKVIGADTKRNCHLNENIEK-GLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDS 84
Cdd:PLN02552  12 MDAVQRRLMFEDE--CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   85 CSSHPLYN--------PAELEEKDAIGVRRAAQRRLQAELGIPGEQISPEDIVFMTIYHHKAKSDRI------WGEHEIC 150
Cdd:PLN02552  90 CCSHPLYGqdpnevdrESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDVThgpdgkWGEHELD 169

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 20978506  151 YLLLVRKN--VTLNPDPSETKSILYLSQEELWELLEREarGEVKVTPWLRTIAERFLYRWWPHLDDVTPFVELHKIHRV 227
Cdd:PLN02552 170 YLLFIRPVrdVKVNPNPDEVADVKYVNREELKEMMRKE--SGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 6-227 2.06e-79

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 238.09  E-value: 2.06e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    6 LDWVDRRQLQRLEemLIVVDENDKVIGADTKRNCHLNENIEK-GLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDS 84
Cdd:PLN02552  12 MDAVQRRLMFEDE--CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   85 CSSHPLYN--------PAELEEKDAIGVRRAAQRRLQAELGIPGEQISPEDIVFMTIYHHKAKSDRI------WGEHEIC 150
Cdd:PLN02552  90 CCSHPLYGqdpnevdrESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDVThgpdgkWGEHELD 169

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 20978506  151 YLLLVRKN--VTLNPDPSETKSILYLSQEELWELLEREarGEVKVTPWLRTIAERFLYRWWPHLDDVTPFVELHKIHRV 227
Cdd:PLN02552 170 YLLFIRPVrdVKVNPNPDEVADVKYVNREELKEMMRKE--SGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 20-202 4.51e-65

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 198.87  E-value: 4.51e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  20 MLIVVDENDKVIGADTKRNCHLNEniekGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYNpaeleek 99
Cdd:cd02885   1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLPG------- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506 100 daIGVRRAAQRRLQAELGIPgeqisPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSQeel 179
Cdd:cd02885  70 --EGVEDAAQRRLREELGIP-----VCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSL--- 139

                       170       180
                ....*....|....*....|...
gi 20978506 180 WELLEREARGEVKVTPWLRTIAE 202
Cdd:cd02885 140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 21-201 1.12e-55

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 174.84  E-value: 1.12e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    21 LIVVDENDKVIGADTKRNCHLNENIekglLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYnpaeleekd 100
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   101 aiGVRRAAQRRLQAELGIPGEQIspeDIVFMTIYHHKAKSDrIWGEHEICYLLLVRKNVTLNPDPsETKSILYLSQEELW 180
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDV---PLTVLPRFSYRARDD-AWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 20978506   181 ELLEREARGevkVTPWLRTIA 201
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 18-200 1.88e-40

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 136.10  E-value: 1.88e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  18 EEMLIVVDENDKVIGADTKRNCHlneniEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLynPAEle 97
Cdd:COG1443   1 EELVDLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPR--AGE-- 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  98 ekdaiGVRRAAQRRLQAELGIPGeqisPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSqe 177
Cdd:COG1443  72 -----TYEEAAVRELEEELGITV----DDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT-- 140

                       170       180
                ....*....|....*....|...
gi 20978506 178 eLWELLEREARGEVKVTPWLRTI 200
Cdd:COG1443 141 -LEELLALLEAGPEAFTPWFRLY 162
NUDIX pfam00293
NUDIX domain;
49-167 4.99e-10

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 55.57  E-value: 4.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    49 LLHRAFSVVLFNTKNRILIQQRSdtKVTFPGYFTdscsshplyNPAELEEKDAiGVRRAAQRRLQAELGIPgeqisPEDI 128
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWWS---------LPGGKVEPGE-TPEEAARRELEEETGLE-----PELL 63

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 20978506   129 VFMTIYHHKAKSDRIWG-EHEICYLLLVRKNVTLNPDPSE 167
Cdd:pfam00293  64 ELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDG 103
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 6-227 2.06e-79

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 238.09  E-value: 2.06e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    6 LDWVDRRQLQRLEemLIVVDENDKVIGADTKRNCHLNENIEK-GLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDS 84
Cdd:PLN02552  12 MDAVQRRLMFEDE--CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   85 CSSHPLYN--------PAELEEKDAIGVRRAAQRRLQAELGIPGEQISPEDIVFMTIYHHKAKSDRI------WGEHEIC 150
Cdd:PLN02552  90 CCSHPLYGqdpnevdrESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDVThgpdgkWGEHELD 169

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 20978506  151 YLLLVRKN--VTLNPDPSETKSILYLSQEELWELLEREarGEVKVTPWLRTIAERFLYRWWPHLDDVTPFVELHKIHRV 227
Cdd:PLN02552 170 YLLFIRPVrdVKVNPNPDEVADVKYVNREELKEMMRKE--SGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 20-202 4.51e-65

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 198.87  E-value: 4.51e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  20 MLIVVDENDKVIGADTKRNCHLNEniekGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYNpaeleek 99
Cdd:cd02885   1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLPG------- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506 100 daIGVRRAAQRRLQAELGIPgeqisPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSQeel 179
Cdd:cd02885  70 --EGVEDAAQRRLREELGIP-----VCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSL--- 139

                       170       180
                ....*....|....*....|...
gi 20978506 180 WELLEREARGEVKVTPWLRTIAE 202
Cdd:cd02885 140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 21-201 1.12e-55

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 174.84  E-value: 1.12e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    21 LIVVDENDKVIGADTKRNCHLNENIekglLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYnpaeleekd 100
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   101 aiGVRRAAQRRLQAELGIPGEQIspeDIVFMTIYHHKAKSDrIWGEHEICYLLLVRKNVTLNPDPsETKSILYLSQEELW 180
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDV---PLTVLPRFSYRARDD-AWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 20978506   181 ELLEREARGevkVTPWLRTIA 201
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 18-200 1.88e-40

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 136.10  E-value: 1.88e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  18 EEMLIVVDENDKVIGADTKRNCHlneniEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLynPAEle 97
Cdd:COG1443   1 EELVDLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPR--AGE-- 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  98 ekdaiGVRRAAQRRLQAELGIPGeqisPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSqe 177
Cdd:COG1443  72 -----TYEEAAVRELEEELGITV----DDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT-- 140

                       170       180
                ....*....|....*....|...
gi 20978506 178 eLWELLEREARGEVKVTPWLRTI 200
Cdd:COG1443 141 -LEELLALLEAGPEAFTPWFRLY 162
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
18-167 9.26e-30

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 109.29  E-value: 9.26e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   18 EEMLIVVDENDKVIGADTKRNCHLNEniekGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLynPAEle 97
Cdd:PRK03759   5 TELVVLLDEQGVPTGTAEKAAAHTAD----TPLHLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQ--PGE-- 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   98 ekdaiGVRRAAQRRLQAELGIPGEQISPEDIVFMtiYHHKAKSDRIwgEHEICYLLLVRKNVTLNPDPSE 167
Cdd:PRK03759  77 -----SLEDAVIRRCREELGVEITDLELVLPDFR--YRATDPNGIV--ENEVCPVFAARVTSALQPNPDE 137
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 23-175 2.49e-20

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467574 [Multi-domain]  Cd Length: 142  Bit Score: 83.38  E-value: 2.49e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  23 VVDENDKVIGADTKRNCHlneniEKGLLHRAFSVVLFNTKN-RILIQQRSDTKVTFPGYFTDSCSSHplYNPAEleekda 101
Cdd:cd04692   3 IVDEDGRPIGVATRSEVH-----RQGLWHRTVHVWLVNPEEgRLLLQKRSANKDDFPGLWDISAAGH--IDAGE------ 69

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 20978506 102 iGVRRAAQRRLQAELGIpgeQISPEDIVFMTIYHHKAKSDRIWGeHEICYLLLVRKNVTLN---PDPSETKSILYLS 175
Cdd:cd04692  70 -TYEEAAVRELEEELGL---TVSPEDLIFLGVIREEVIGGDFID-NEFVHVYLYETDRPLEefkLQPEEVAGVVFVD 141
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 23-175 2.04e-15

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467578 [Multi-domain]  Cd Length: 157  Bit Score: 70.73  E-value: 2.04e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  23 VVDENDKVIGADTKrnchlNENIEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFtDSCSShplynpaeleekdai 102
Cdd:cd04697   3 IVDENNEVVGAATR-----AEMRRQKLIHRATYIVVRNAAGRLLVQKRTMDKDYCPGYL-DPATG--------------- 61

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506 103 GV-------RRAAQRRLQAELGIPGEQISPedivFMTIYHHKAKSdRIWGEheiCYLLLVRKNVTlnPDPSETKSILYLS 175
Cdd:cd04697  62 GVvgagesyEENARRELEEELGIDGVPLRP----LFTFYYEDDRS-RVWGA---LFECVYDGPLK--LQPEEVAEVDWMS 131
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 23-175 3.31e-14

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467575 [Multi-domain]  Cd Length: 157  Bit Score: 67.55  E-value: 3.31e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  23 VVDENDKVIGADTKRNchlnENIEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLY--NPAEleekd 100
Cdd:cd04693   5 LYDENRNKTGRTHRRG----EPLPEGEYHLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAgeTSLE----- 75

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20978506 101 aigvrrAAQRRLQAELGIpgeQISPEDIVFMTIYHHkaksdriwgEHEICYLLLVRKNVTLN---PDPSETKSILYLS 175
Cdd:cd04693  76 ------AAIRELKEELGI---DLDADELRPILTIRF---------DNGFDDIYLFRKDVDIEdltLQKEEVQDVKWVT 135
NUDIX pfam00293
NUDIX domain;
49-167 4.99e-10

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 55.57  E-value: 4.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    49 LLHRAFSVVLFNTKNRILIQQRSdtKVTFPGYFTdscsshplyNPAELEEKDAiGVRRAAQRRLQAELGIPgeqisPEDI 128
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWWS---------LPGGKVEPGE-TPEEAARRELEEETGLE-----PELL 63

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 20978506   129 VFMTIYHHKAKSDRIWG-EHEICYLLLVRKNVTLNPDPSE 167
Cdd:pfam00293  64 ELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDG 103
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 7-145 1.68e-08

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 52.50  E-value: 1.68e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506    7 DWVDrrqlqrleemliVVDENDKVIG----ADTKRNChlneniekgLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFt 82
Cdd:PRK15393  10 EWVD------------IVNENNEVIAqasrEQMRAQC---------LRHRATYIVVHDGMGKILVQRRTETKDFLPGML- 67

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20978506   83 DSCSSHPLYNPAELEEkdaigvrrAAQRRLQAELGIPGEQISPEDivfmtIYHHKAKSDRIWG 145
Cdd:PRK15393  68 DATAGGVVQAGEQLLE--------SARREAEEELGIAGVPFAEHG-----QFYFEDENCRVWG 117
PLN02791 PLN02791
Nudix hydrolase homolog
 17-127 1.72e-03

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 39.03  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506   17 LEEMLIVVDENDKVIGADTKRNchlnENIEKGLLHRAFSVVLF-NTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYNPAE 95
Cdd:PLN02791   2 MEEHLDVLTAAGEKTGVSKPRG----EVHRDGDYHRAVHVWIYsESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTS 77

                         90       100       110
                 ....*....|....*....|....*....|..
gi 20978506   96 LeekdaigvrRAAQRRLQAELGIpgeqISPED 127
Cdd:PLN02791  78 L---------LSAQRELEEELGI----ILPKD 96
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 52-134 9.84e-03

NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus radiodurans protein DR_0079 is one of 21 NUDIX hydrolases that it encodes, and it has been observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP), and for their corresponding deoxyribose nucleotides, dCDP and dCTP, to a lesser degree. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467602 [Multi-domain]  Cd Length: 121  Bit Score: 34.88  E-value: 9.84e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20978506  52 RAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPL----YNPA---ELEEKDAIGVRRAAQRrlqaELGipgeQIS 124
Cdd:cd24154   3 RVVNAFLINSQGQLWIPRRTADKRIFPLALDMSVGGHVSsgetYEQAfvrELQEELNLDLDQLSYR----VLG----KLT 74

                        90
                ....*....|...
gi 20978506 125 PED---IVFMTIY 134
Cdd:cd24154  75 PYEhgvSAFMKVY 87
 
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.
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