2OOG


Conserved Protein Domain Family
GDPD_SaGlpQ_like
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cd08601: GDPD_SaGlpQ_like 
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Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Links
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Statistics
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PSSM-Id: 176543
Aligned: 13 rows
Threshold Bit Score: 313.484
Created: 16-Dec-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Conserved site includes 2 residues -Click on image for an interactive view with Cn3D
Feature 1:catalytic site [active site]
Evidence:
  • Structure:2OOG;The catalytic site of Staphylococcus aureus glycerophosphoryl diester phosphodiesterase consists of two conserved histidine residues, which serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
    - View structure with Cn3D
  • Citation:PMID 6304089
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                   #                                          #                               
2OOG_A              24 FTTIAHRGASGYAPEHTFQAYDKSHNElKASYIEIDLQRTKDGHLVAMHDETVNRTTNG--------------------- 82  Staphyloc...
YP_002560788         5 NVVIAHRGASGYAPEHTFASYDKSHYDmHADYIELDIHMTLDNEIIVMHDESIERTALT--------------------- 63  Macrococc...
NP_833229           38 FLNIAHRGASGHAPEHTFASYDLVKKM-KADYLELDIQLTKDGQLIAMHDTAVDRTTNG--------------------- 95  Bacillus ...
P37965              38 ILTVAHRGASGYVPEHTILSYETAQKM-KADFIELDLQMTKDGKLIVMHDEKLDRTTNG--------------------- 95  Bacillus ...
NP_979008           39 IKNIAHRGASAYAPEHTIAAYTLGQQL-KGDYIEIDLQMTKDGYLVAMHDETLNRTTNG--------------------- 96  Bacillus ...
REF_jgi:Pjdr2_2736  45 AAIIAHRGASGYAPEHTLAAFRSAIEA-GADFIEIDLQLTKDGQIVAMHDNTVNRTTNA--------------------- 102 Paenibaci...
YP_643095           22 VLNVGHRGASGYAPEHTFTAYDLALRM-GADYIEQDLQMTRDGVLVVLHDETLDRTARPtaesg---------------- 84  Rubrobact...
YP_002634037        55 NVAIAHRGASGYAPEHTFFAYDKAKNElGADYIELDLQMTKDGNLIAMHDETVDRTTGGk-------------------- 114 Staphyloc...
EET72077            46 IGVIAHRGASGYAPEHTLTAYKKAIQM-KADYIELDLHMTKDGELVAIHDATLSRTTNAeevy----------------- 107 Geobacill...
ZP_03478729         24 PSIIAHRGTCYWAPEGTEAAMRWARNA-GATYLECDLQRTKDGYLVLFHDLRLTRTSDIdsky----------------- 85  Parabacte...
NP_793241           40 PAAIAHRGASFDAPEETIPAYTLARDL-GADYLEMDIQRTKDGVLIALHDDVLERTTNIaqvf----------------- 101 Pseudomon...
ZP_05882481         53 NAIIAHRGDSYNAPEATLPAYQLACEF-GADYLEVDLQRSKDGVLIAVHDNNLRNKTNIaeiy----------------- 114 Vibrio me...
ZP_02436428         57 YAVMAHRGSTFWAPEETESAWRWAREM-GADYLESDLQCTKDGVILANHDDNLKRTTNIenvyselvpatrkafymrhgm 135 Bacteroid...

Feature 1                                                                                              
2OOG_A              83 -----------------HGKVEDYTLDELKQLDAGSWFNKKYPKYARASYk--NAKVPTLDEILERYGp----------- 132 Staphyloc...
YP_002560788        64 -----------------PGIIKEMTLQEIKKLTIGKWFNEKFPELKEDYYa--EQLVPTLEDVFERYKd----------- 113 Macrococc...
NP_833229           96 -----------------TGEVRDKTLSEIKSLDAGSWFNKAYPEKAKQEYv--GQKVPTLEEIFQKYGr----------- 145 Bacillus ...
P37965              96 -----------------MGWVKDHTLADIKKLDAGSWFNEAYPEKAKPQYv--GLKVPTLEEVLDRFGk----------- 145 Bacillus ...
NP_979008           97 -----------------TGLVKEHTLEEIKQLNAGSTYNKKYPNLAKKEYe--NAKVPTLEEVIEVFGh----------- 146 Bacillus ...
REF_jgi:Pjdr2_2736 103 -----------------KGKVGAMTLDVIKQLDAGSWFNKHHPMYAREEYa--RQQVPSLTDIFTAFGr----------- 152 Paenibaci...
YP_643095           85 -------------pgdcTGLVREKTLAQIKTCDVGSWFNEAYPQYARPEYv--GLRIPTLEEVFQRYRk----------- 138 Rubrobact...
YP_002634037       115 ----------------fHGPVKNYTTAQLKQMDVGSWFNQKNPQYANPKYa--GAKVPTLDEILTRYGp----------- 165 Staphyloc...
EET72077           108 -------------pgrsPWRVKDFTLSEIKQLDAGSWFNDAYPEYAKKQYs--NEKIPTLQETIDYIKqkd--------- 163 Geobacill...
ZP_03478729         86 -------------perkNVAISDLTLEELFKLDMGSWFNYTYPSNARSSFs--KLDILTLEDLTMIAEgyriqrdtfqkr 150 Parabacte...
NP_793241          102 -------------ptrvKDPVSTFTLAELKQLDAGSWFNKAYPDRARDSYn--GLQILTLDEVIDIAEgga--------- 157 Pseudomon...
ZP_05882481        115 -------------pgraDSPVSSFTWAELEKLDAGSWFNSAYPERARESYr--GLQLMTLDQVREVAEncs--------- 170 Vibrio me...
ZP_02436428        136 seaeaeklveadkasfrPYYAMSYMYEELLALDAGSWFNETSIEQARESFseqHQYISALEDQIRYAEgkmlkrdvnger 215 Bacteroid...

Feature 1                                                                                              
2OOG_A             133 --------------------------------nANYYIETKSPDVYP-GMEEQLLASLKKHHLlnnn------------- 166 Staphyloc...
YP_002560788       114 ---------------------------------ANYYIETKSPDIYP-GMESLLIDMLDEYGLisdt------------- 146 Macrococc...
NP_833229          146 --------------------------------sMKYYIETKSPDVYP-GMEEKLLALLQKYNLvgqn------------- 179 Bacillus ...
P37965             146 --------------------------------hANYYIETKSPDTYP-GMEEKLIASLQKHKLlgkh------------- 179 Bacillus ...
NP_979008          147 --------------------------------dANYYIETKSPDEYP-EMEEKLLEIINHYEIq---------------- 177 Bacillus ...
REF_jgi:Pjdr2_2736 153 --------------------------------eTHYILEIKDSTYNP-GIEEKLLETIYQYRLe---------------- 183 Paenibaci...
YP_643095          139 --------------------------------sVNYYIETKSPEAAP-GMEEELLRLMDEYGLtrpa------------- 172 Rubrobact...
YP_002634037       166 --------------------------------dTNYYIETKSPDVYP-AMEEKLLDTLNKHGMltsd------------- 199 Staphyloc...
EET72077           164 -------------------------------anAALYIETKAPNVYP-GMEEKLVDILKKNGYlq--------------- 196 Geobacill...
ZP_03478729        151 iykkin----------griitlyepdpadngnrPGIYTETKEPDLYP-GIELDLKKELERLGWyadnvsnlksiktkpgh 219 Parabacte...
NP_793241          158 -------------------------------nkPGLYIETKVPNKFP-GVEADLKKVLAKRGWltqrpaaaa------gh 199 Pseudomon...
ZP_05882481        171 -------------------------------hqPGLYIETKLPELFP-GIEADLRANLQQHGWldk-------------- 204 Vibrio me...
ZP_02436428        216 iytvtgtwnpdkprdcltykfeyvddpqdtgnrPGVYIEFKESWLNPsDFEKRVYNKLDELGWniitkpcdgepfyknnk 295 Bacteroid...

Feature 1                                                                                              
2OOG_A             167 ---klknGHVMIQSFSDESLKKIHRQNk-HVPLVKLVDKGElqq-----------------------------fnDQRLK 213 Staphyloc...
YP_002560788       147 ---rlknRQTVIQSFSLESLIKVNQLVp-DMPLLLLAKKGVlre-----------------------------msDEDLK 193 Macrococc...
NP_833229          180 ----mssSRVMIQSFSKDSLKKIHSMNe-NIPLVQLLWYYPnenneivews--------------githepksvtNDDFQ 240 Bacillus ...
P37965             180 ----skpGQVIIQSFSKESLVKVHQLQp-NLPTVQLLEAKQmas-----------------------------mtDAALE 225 Bacillus ...
NP_979008          178 -------DKVIIQSFSEESLQKIHNLNv-NIPLVQLLSYKKavq-----------------------------ltELEIK 220 Bacillus ...
REF_jgi:Pjdr2_2736 184 -------DQVIIQSFDAKSLKKIHRLNd-RIELLQLMWYNTpar-----------------------------isSVSLN 226 Paenibaci...
YP_643095          173 ----aerWQVLIQSFSPASLQKVHALDp-SLPLIQLFSGTEtse-----------------------------tiRAKLD 218 Rubrobact...
YP_002634037       200 ---klknGQIVIQSFSQESLLKMKKLNp-NIPLIQLTDVLEipr-----------------------------ytDKDLD 246 Staphyloc...
EET72077           197 ------pGKVIFQSFSAASLRKLREIVpkGIPLIQLYSPAMiqg----------------------------qnlDDVLD 242 Geobacill...
ZP_03478729        220 iyiantpARIVVQTFSQASLKKLRQSFprLIPMCYLIGIAAkdnvn-------------------------ketyEKWIN 274 Parabacte...
NP_793241          200 vnvahmpGRVVLQTFEKQSLELLQKEMp-QVPKVLLLWIGEgsiepkssvafkdsgakdkasyyaaqevkspeefQKWID 278 Pseudomon...
ZP_05882481        205 ----emkGKVILQTFEKESLIQLQAEMp-DIPKVLLLWTGDgyidmkptepkqddes--waayyarvqvasksayEEWID 277 Vibrio me...
ZP_02436428        296 vnvgntnGKVILQTFSLESLRRTAEEFkgKIPMCFLLWEGNgatdlkh---------------------dtpqgyASFIN 354 Bacteroid...

Feature 1                                                                                              
2OOG_A             214 EIRS-YAIGLGPDYTDLt----------------EQNTHHLKDlGFIVHPYTVNe---KADMLRLNKY------------ 261 Staphyloc...
YP_002560788       194 QIHT-FVYAVGPSIADLd----------------ETLISRMHNfGYLVLPYTLNk---EADMERLINA------------ 241 Macrococc...
NP_833229          241 EIKK-YAAGIGPNLRNDngel----------iidESYMKMARKnGLLIHPYTINe---KPDMRLLIKW------------ 294 Bacillus ...
P37965             226 EIKT-YAVGAGPDYKALn----------------QENVRMIRShGLLLHPYTVNn---EADMHRLLDW------------ 273 Bacillus ...
NP_979008          221 KYKT-YCIGLGMNYKYId----------------SAYVKRIKKhGLEVHPFTVDn---EQDMKKLLLW------------ 268 Bacillus ...
REF_jgi:Pjdr2_2736 227 KIKK-YATGISPNFPKIn----------------AAYVHKVQKsGLRIYPYTVNy---QLNMDRALSW------------ 274 Paenibaci...
YP_643095          219 ATAA-YAVGIGPSKDDVd----------------AELVGAAHArCLDVHPYTVNe---SAEMEGLIAT------------ 266 Rubrobact...
YP_002634037       247 YIAS-YADGVGPEYHDAt----------------PAQVERLHQhGLLVHPYTANt---KLAMQNLINA------------ 294 Staphyloc...
EET72077           243 QAAE-YAEGVGPELSLVt----------------PEFVQKAHErHLIVHPFTINt---KEEMQKQLSL------------ 290 Geobacill...
ZP_03478729        275 FAIEqGAVIIGPSIYEKdgllg--------dllkPWMYDLIKEkGLLIHAYTFK----NREQIINYLD------------ 330 Parabacte...
NP_793241          279 WAKAhGAIGTGPSSQLAqggdqs-----ymdlvkPWMNNLTHEkGMVIHPYTVDd---AADFKRIRND------------ 338 Pseudomon...
ZP_05882481        278 FAKDnGAIGVGPSGTQTnfadswssnfsymdlakPWMIEMNQQkGLVTHIYTLDd---AEDLIRYRDR------------ 342 Vibrio me...
ZP_02436428        355 LGLEyKAHIIGPCIAGApndyp--------emnaPWQAYLIKKsGMLNHPYSFDsyaqMGKYFGQYNWgntvqydellhg 426 Bacteroid...

Feature 1                                  
2OOG_A             262 -GVDGVFTNFA-DKYKEVIK 279 Staphylococcus aureus
YP_002560788       242 -GIDGAFTNFP-DVLRKQFR 259 Macrococcus caseolyticus JCSC5402
NP_833229          295 -GATGMFTNYP-DRLHSVLK 312 Bacillus cereus ATCC 14579
P37965             274 -GVTGVFTNYP-DLFHKVKK 291 Bacillus subtilis
NP_979008          269 -GVDGMFTNYP-DRLHSLLK 286 Bacillus cereus ATCC 10987
REF_jgi:Pjdr2_2736 275 -GVDGIYTDYP-DRFREVLQ 292 Paenibacillus sp. JDR-2
YP_643095          267 -GVDGMFTNFP-DRLDAVLG 284 Rubrobacter xylanophilus DSM 9941
YP_002634037       295 -NVDGAFSNYI-DQYMQLRD 312 Staphylococcus carnosus subsp. carnosus TM300
EET72077           291 -GVDGMFTNYP-DRLVSLNK 308 Geobacillus sp. Y4.1MC1
ZP_03478729        331 -MADGFFTNEAdDLLSFLLK 349 Parabacteroides johnsonii DSM 18315
NP_793241          339 -GVDGFFTNRTaELLKFYDR 357 Pseudomonas syringae pv. tomato str. DC3000
ZP_05882481        343 -GVTGFFTNRP-NLAVEVLT 360 Vibrio metschnikovii CIP 69.14
ZP_02436428        427 iYGDGLFTNRSeMSLKYLID 446 Bacteroides stercoris ATCC 43183

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