Conserved Protein Domain Family
GDPD_like_3
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cd08585: GDPD_like_3 
Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity with Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Links
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Statistics
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PSSM-Id: 176527
Aligned: 12 rows
Threshold Bit Score: 272.274
Created: 22-Feb-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
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Conserved Features/SitesClick to see Conserved Features Help
 
Feature 1:catalytic site [active site]
Evidence:
  • Comment:The catalytic mechanism of glycerophosphodiester phosphodiesterases is based on the metal ion-dependent general acid-base reaction.
  • Comment:Based on structure evidence and site-directed mutagenesis of Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase, the catalytic site consists of two conserved histidine residues which serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                #                                           #                           
NP_539736     11 WLKKRPIAHRGLHdqnktcWENTLSAFDAAAKaGFAIECDAHLTrDGGVVVFHDddLKRLAGCEGRIcelttdEATALHI 90  Brucella melite...
NP_420960     18 ALFDRPIAHRGLWsrd-gaPENSLGAFQAACAhDYGIELDVQLTaDGDAVVFHDerLERMTGVEGRVrdhtaaELGALAL 96  Caulobacter cre...
YP_001102515   6 WLHDRPIAHRGRYdesagvPENSLAAFRAAVElGTPFEFDVQLTaDGVAVVAHDanLRRVTGEDVLVaesthaRIRRLRT 85  Saccharopolyspo...
YP_760983      6 ALKDFAYAHRGLWtkd-glPENSLGSFSAAADaGLGIELDLRPSaDGEVMVFHDplLQRMTGAEGQFenfpasTLKTHRL 84  Hyphomonas nept...
YP_003179311 212 EIARHRYAHRGLYnneagiPENSLLAFRTACEkGFGSEVDVHLTaDNRLVVVHDsaLDRLCGVQKIVeestleELRGLRL 291 Atopobium parvu...
ZP_05980739   35 PFCGRSYAHRGLFgaqqrpPENSLPAFAAAARsGYGIELDVQFTeDRQLVVFHDdtLDRMTPGKGGVsstpwpVVSALPL 114 Subdoligranulum...
ZP_02234369   31 AFHGIMFAHRGLHskthgiPENSMSAFRAAIQkNYGIELDLHLTrDGELVVFHDdnLKRVCGRPERPedltaaELTKCTL 110 Dorea formicige...
ZP_05130479   39 WVKNTKISHRGLHnnd-diPENSLKAYKKSIDkNVAIELDVQLTkDNKVVVFHDynLERMTGSNKNVneleyiDILDLKL 117 Clostridium sp....
NP_948477      6 WLTARPVAHRGLHdrargiVENMPGAISAAITgNFSIEVDIQLTaDGEAMVHHDdnLGRLTDGAGPLlgmtaaQLRQVPF 85  Rhodopseudomona...
NP_385598      6 WLKAQPIAHRGFHdmnrevWENTLSAFARAAEaGFAIECDLQFAaDSVPVVFHDhdLQRLCGIRGDVraktsaELGLLSI 85  Sinorhizobium m...
NP_102420      6 WLTARPVAHRGFHdmnktrWENTLSAFTAAAErDYAIECDVHLSsDGVPIIIHDddLKRLTGQDGFVwqrsaaELTALKV 85  Mesorhizobium l...
ZP_06367969    2 WLAKQPIAHRGMYdrs-gvPENSIPAFERCVAaGTPIELDVRLTrDGQVVVFHDagLKRLCNVDALVtalsyqELAALKL 80  Desulfovibrio s...

Feature 1                                                                                        
NP_539736     91 GGTaDHVPTLRQMLDLVd------GRVPLVIELKgieg----rddgLVAAVAKELSpYKGEAAIMSFDHhLIRRFTadaP 160 Brucella melite...
NP_420960     97 KGTdETIPTLAEALTVIg------HRAMVHIELKtpfg----evgpLEKRVSEILIdHNGPTAIIGFNPySHAWFAdhhP 166 Caulobacter cre...
YP_001102515  86 GCGgEPVPTLDDVLEVAg------GQVPVLVDVRrwggh---ggtdLERVVAASLRgYRGAVALQSFDPrAVLRLRrltA 156 Saccharopolyspo...
YP_760983     85 NGGdEPVPSFDDLLSFWp------QDLPVLAEMKidgst---dpmaFAQTVGARLMdWPGLAAAMSFSDiAVRALP---D 152 Hyphomonas nept...
YP_003179311 292 LATdEQIPTFEEVLEVYawsgsgeLPAPLIIEAKtchn----naeqLTEKIMQALDlRPVRACIESFDPrVLQWLRqnrP 367 Atopobium parvu...
ZP_05980739  115 AGSgEHAPLFSEVLHAVas---anPATPLIVEIKscyeyrgrylleLCRAVLAALKhYPGPYCIESFDPrVVRLVRilaP 191 Subdoligranulum...
ZP_02234369  111 LGTkEHIPLFRDVLALVn------DQVPLLVELKiper-----nmqICQKAYEMLRsYHGAFLLESFNSeGLYWFRknaP 179 Dorea formicige...
ZP_05130479  118 LNTnEYIPTLNEVLELId------GKVPLLIEIKnedk-----vgiLESEVYNIIKdYKGDIAVQAFNPfVLSWFKknaP 186 Clostridium sp....
NP_948477     86 KDTpERMMSVDELFDLVa------GRAALVIELKshfd----gdrkLARRLLQVLDsYKGPVAAMSFDPdQVLALRqlaP 155 Rhodopseudomona...
NP_385598     86 GGTrDKVPTLKQMLRLVa------GRVPLIIELKgrkg----ddegFAAAVLETLEgYDGHVALMSFDHwLLRDLKeldA 155 Sinorhizobium m...
NP_102420     86 GGTsDRVPTLQEALDLVd------GRVPMVVELKgipg----rdegLVARVGNMLKrYKGKAAIMSFDHwLIREFPkhaP 155 Mesorhizobium l...
ZP_06367969   81 LGSrEKIPLLADVLAKVa------GKVPLLVELKsqgr-----tgaLERQVAAALAgYRGAYAVQSFTPwTVGWFRrnrP 149 Desulfovibrio s...

Feature 1                                                                                        
NP_539736    161 GIPGGLTAEGtrmqdfek------------hfsmlahgISFVSYNVHHLPnpfVTFVRERlQIPVISWTVRdrEMQKYSD 228 Brucella melite...
NP_420960    167 QILRGLDSYGwndegarhvapemr-ksmaalehveiarPDFLALGLDMLPspkADVLRAK-GMPVIAWTVRtpEQWAAIQ 244 Caulobacter cre...
YP_001102515 157 DHPVGQASGSlpsaapplrwi------grsmvsnvltrPDFVSYELAALPcwfADRWRTR-TRPLIAFTAHsrAEAGRAL 229 Saccharopolyspo...
YP_760983    153 GLMRGQLIGPsnqfgdayfd--------sfarramadgIDYLAVHYTDAAr--AAAATADrGMPVVVWTVRteADLAALK 222 Hyphomonas nept...
YP_003179311 368 EMLRGQLSENflidrqtrhmniatragatalfgnsvgrPDFIAYKFEDRKnpfVKLACNTmGAHLITWTVRseEDMIASE 447 Atopobium parvu...
ZP_05980739  192 GVVRGQLADSyrnhrrigtprvaa-yllshcfgnllarPDFIAWCPDKRNw-aIRLCAAL-GAMTVMWTAVpeYDIARLE 268 Subdoligranulum...
ZP_02234369  180 EVLRGQLSSRltkeksdvswflr--ffvenlwcnflgrPDFIAYKLTDLPkltVTLLRIFsGTTIAVWTLRtkDAIHEGK 257 Dorea formicige...
ZP_05130479  187 EIPRGQLSGSfddsdlpkykkf----llknlllnfeskPAFIAYEVDYLPkavVKFQRNR-NVPILGWTVKstTDLEKVK 261 Clostridium sp....
NP_948477    156 KLTRGITAERsyddaywaklneaqrdpmvalkhglrtqPHFVAYRIDDLPapaPWIARNLfGCALLSWTVRtpEQRARAS 235 Rhodopseudomona...
NP_385598    156 PYPLGLTAEGsnpetffv------------heeamhlgLDFISYHYGHLPnpfTEKERAL-GRTLITWTVRdrQAQEHTF 222 Sinorhizobium m...
NP_102420    156 GIPAGLTAYGkdlkliea------------hfsmlaheLSFTSYAAGDLPnpfVSFVREKlKMPVITWTVHdqPAIDLTF 223 Mesorhizobium l...
ZP_06367969  150 GMLRGQLTCTyddrkdmhcinky---ilknmlyniltkPLFLSVHKNMLHgsfLTRLRQS-GLPVLVWTITdkREAAFCQ 225 Desulfovibrio s...

Feature 1                  
NP_539736    229 lnVDQITFEG 238 Brucella melitensis 16M
NP_420960    245 ahCDNLIFEG 254 Caulobacter crescentus CB15
YP_001102515 230 qvADNYFYAG 239 Saccharopolyspora erythraea NRRL 2338
YP_760983    223 pyGAAIIFEH 232 Hyphomonas neptunium ATCC 15444
YP_003179311 448 leGAPVIFEG 457 Atopobium parvulum DSM 20469
ZP_05980739  269 reNDAVIFQW 278 Subdoligranulum variabile DSM 15176
ZP_02234369  258 qeYDIQIFEN 267 Dorea formicigenerans ATCC 27755
ZP_05130479  262 enCDNIIYEE 271 Clostridium sp. 7_2_43FAA
NP_948477    236 ryADQMIFEG 245 Rhodopseudomonas palustris CGA009
NP_385598    223 anADQMTFEG 232 Sinorhizobium meliloti 1021
NP_102420    224 kyADQMTFEG 233 Mesorhizobium loti MAFF303099
ZP_06367969  226 qlGFNYIFDP 235 Desulfovibrio sp. FW1012B

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