3L12,3CH0


Conserved Protein Domain Family
GDPD_SpGDE_like

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cd08567: GDPD_SpGDE_like 
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Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Statistics
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PSSM-Id: 176510
View PSSM: cd08567
Aligned: 17 rows
Threshold Bit Score: 293.45
Threshold Setting Gi: 42524227
Created: 20-Oct-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 2 residues -Click on image for an interactive view with Cn3D
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.
  • Structure:3L12; The catalytic site of Silicibacter pomeroyi glycerophosphodiester phosphodiesterase consists of two conserved histidine residues, which may serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
    View structure with Cn3D
  • Citation:PMID 6304089

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             #                                         #                                
3L12_A        18 VRVIGHRGARGvxPENTLEGFAFTLAAGVRALEFDVVXTADGVPVVTHNHHLANAXTrdgqghw-----ltgaerqVAEX 92  Silicibacter po...
NP_969607     52 MEVHGHRGIDGy-PNNTVASFKAAYDAGADTAELDLMITGDDQIVTAHDPIPNIKAErcslhgk------slekaaLRNM 124 Bdellovibrio ba...
NP_660985      3 FEIQAHRGARAfyPDNTLQAFCKAADLGCRVIELDLNVSRDLRMVVSHDPWVSCASGdnps------------khyLYAM 70  Chlorobium tepi...
YP_548310     22 FDLQGHRGARAiaPENTLEGFAQALSYGVTTLELDIAITQDGVLVISHDSALNPDITrgpdgkf-----lqtrgpvISSL 96  Polaromonas sp....
NP_773224     38 LDLEAHRGGRAllPENTLPAFANALSMGVDTLELDVGVTADGAVIISHERGLNPDLArdangay-----vappgtpFVRL 112 Bradyrhizobium ...
ZP_01743805   18 VRLHGHRGARGiwPENTLIGFQGAMDMGIQAIELDVLLTKDNVPVVTHNPKLMIATSrdkngqw-----lsnenlnVAEL 92  Rhodobacterales...
YP_001233703  11 MALFGHRGARGllPENTLEGFASIAALDLTGAEFDVGLTADGVAVVHHDPRLNPDIArdadgawl----apdaaplLRER 86  Acidiphilium cr...
ZP_04989540   23 INIYAHRGYRPiaPENTLPAYTEAMRIGVDVIDMDINMTKDKVLVVTHDLTLNPDLTkdengnw------isektpIKDL 96  Francisella tul...
YP_003297842   6 IEVHGHRGARGlrPENTLPGFAHALELGVDVIELDVGLTADGVVVVNHDQSLSPVTTadtapvvpgdplfpyvgreLRDL 85  Thermomonospora...
NP_927324      9 PLVIAHRGCRAqvPENTLPAFERALDLRVDGIEMDLHLSGDGQVLVSHDPRPLPGKCrlstgpl------pveppcWGEL 82  Gloeobacter vio...
Feature 1                                                                                        
3L12_A        93 TYAEIRALDVGgldgrt----vygrrFPDQAflt-------gihVPRLGELLDLCAgyg---------dqaPYLLLELKS 152 Silicibacter po...
NP_969607    125 SSTEVAQIRCGer------------hFSEARte----------pIPLLRDVFDAFKdskv-------agkpTRLNIEIKY 175 Bdellovibrio ba...
NP_660985     71 NYDEIAQLDCGeas----------adFPFRHsvr--------avRPILSEVFGTVEeqlrra----grpgeMIYNLEVKS 128 Chlorobium tepi...
YP_548310     97 TFDELSRYDVGrikpgt----qyarlYPDQRgmd-------gvrIPRLSALFALVKksg---------ndrVRFAIETKV 156 Polaromonas sp....
NP_773224    113 RLEEVGSYDVGqlrpds----ayakqFPEQRavp-------gtrIPTLRQLFALVRksg---------ndrVRFNIETKI 172 Bradyrhizobium ...
ZP_01743805   93 HFDELRQIDVGgilags----tyaslYPDQAflf-------gqnIPTLEDIARLVCrda---------yqnVWMNLEIKS 152 Rhodobacterales...
YP_001233703  87 TLADLGSFDVGrlrpgs----dyaarYPEQTpad-------garIPTLDAVIAALSg--------------RDLLIEVKT 141 Acidiphilium cr...
ZP_04989540   97 TLAQVKKYTVGyikpds----atakmYPNHIgmd-------nvhMPTLEEVINYVKsnv---------gsrVRLQIEIKT 156 Francisella tul...
YP_003297842  86 TLAQIKTVDAGvrrlgpg--qdcdpfLLTQLplp-------gtrLPTLAEVCDLLQgl-----------eeVDPAVELKT 145 Thermomonospora...
NP_927324     83 ELSTIQDNYIAdcqfelgsaerpktlYTGRIapllmknvasvfvPPTLEQVFALLAaygqlgaeqalylqsIRIFLEIKR 162 Gloeobacter vio...
Feature 1                                                                                        
3L12_A       153 DPalx--hdhAARAEXVAAVLADVRRYrx-ePRTVXHSFDWALLGECRRQAPdLPTSYLSQLpenaddpgedsak----- 224 Silicibacter po...
NP_969607    176 FKdqv--qyfPPEDQYLDLIIKEIRQSgwsqDRFFVQSFNHQTLKNLKAKAPdIEVVPLIWDar---------------- 237 Bdellovibrio ba...
NP_660985    129 WPgldg-aahPLPEEYAALVTREIAASel-eRRVRLQSFDDRILVAARNLAPtLCYGLLVEEra---------------- 190 Chlorobium tepi...
YP_548310    157 SPlap--qdtMEVEAFTRAVLGSIREAgv-aPRSSVLSFEWRSLQVVQREAPeIPTVYLTAQqrfmdnieadkagv---s 230 Polaromonas sp....
NP_773224    173 DPnhp--desLDPQGFVTKLLGLIEAEkf-sERVMIQSFDWRTLQLVQQQAPtIPTVYLTLQrgsgqtvvldkatn---- 245 Bradyrhizobium ...
ZP_01743805  153 TPlgn--hvmPSPKALAENVLSLIAEYgl-dSRTIIQCFDWRVLREVERIAPsIPRSYLTYMdcpapvmapniyvd---s 226 Rhodobacterales...
YP_001233703 142 FPdrp--gltAPPERIAQAVIACLNRHda-lDRAVLFAFDWRVLRAAAAAAPaLRRCCLTEPetvsagplwld------- 211 Acidiphilium cr...
ZP_04989540  157 NPydp--easWSAQEMAEALNKVLLKTgm-tDNVEVQSFEWQALVDLQKLNPkVKTAYLTDHttepmnaeqakqltdyqk 233 Francisella tul...
YP_003297842 146 DPgw----pdDEVRRFVLAVAEVLDSFgl-lSRARLLAFDWRVLAEARIHVPqAARVALVERktladgtaw--------- 211 Thermomonospora...
NP_927324    163 APfydalwlgPHGERFEQCVASAIERSsf-cKNVVVLSFVPRALQAIGQCNRsIRTALLTAHtp---------------- 225 Gloeobacter vio...
Feature 1                                                                                        
3L12_A       225 -pvgpdydrxtesLPQAVASAGG---QLWCPYFldvtPELVAEAHDLGLIVLTWTV-------NEPEDIRRXATTGVDGI 293 Silicibacter po...
NP_969607    238 ------------gALDAATNLGSrlvTTGWPQLt---PEVVFGLHQKGIRVVAWTP-------NTVEELKWVIASGADGV 295 Bdellovibrio ba...
NP_660985    191 ------------vFDRFPERPGFv-pEYVNPRLdlvdESLVSWLHGLGAKVVVWTV-------NHPEDMLRMKRFGADGI 250 Chlorobium tepi...
YP_548310    231 pwtaglrykdhgsVPRMIKAAGG---HTWSAYHgdltAAKVKEAHDLGLKVLAWTV-------NDPGLMARMMDMGVDGI 300 Polaromonas sp....
NP_773224    246 wtagfspadhggsLPRTIKAAGG---AIWSPYFgdvtAALVSEAHGLGLRVVVWTV-------NKPEDMTRMIEIGVDGI 315 Bradyrhizobium ...
ZP_01743805  227 pwmagtsyndkseLCEIIVELGG---AVWSPFHkdltMRDVERAQSLGLIVNAWTV-------NEKADFDRMIEFGVDGI 296 Rhodobacterales...
YP_001233703 212 ---gcdlgafggnLPRAVAATGA---VCWAPFHatleEDDVREAHALGLAVLPWTV-------NAPEAFDRMIRLGVDGM 278 Acidiphilium cr...
ZP_04989540  234 wtapldpkdynynYPLMVKKLGG---TFWEPYEkdltKKDVEEAHKLGVKVVTWGWtedegsdFNYEVINNLIDWKVDGI 310 Francisella tul...
YP_003297842 212 -----laglsaadPAAAAADAGA---NVLSPEHdlvtSRLVHDAHGRGLRVSVWTV-------NDPVDMARFIEYGVDAI 276 Thermomonospora...
NP_927324    226 -----------vnLLTDMQHLNA---QLWCPYYqsidRSAVEIAQAAGLQVIPWTV-------NDAKEMAVLTEWRVNGL 284 Gloeobacter vio...
Feature 1               
3L12_A       294 VTDYPGR 300 Silicibacter pomeroyi
NP_969607    296 ITDRADL 302 Bdellovibrio bacteriovorus HD100
NP_660985    251 ITDHPEV 257 Chlorobium tepidum TLS
YP_548310    301 VSDRPDL 307 Polaromonas sp. JS666
NP_773224    316 ISDRPDL 322 Bradyrhizobium japonicum USDA 110
ZP_01743805  297 ITDYPNR 303 Rhodobacterales bacterium HTCC2150
YP_001233703 279 ISDRPDL 285 Acidiphilium cryptum JF-5
ZP_04989540  311 ITDRPDI 317 Francisella tularensis subsp. novicida GA99-3548
YP_003297842 277 VTDYPDR 283 Thermomonospora curvata DSM 43183
NP_927324    285 VTDVPDL 291 Gloeobacter violaceus PCC 7421

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