Conserved Protein Domain Family
GDPD_like_2

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cd08582: GDPD_like_2 
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 to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Statistics
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PSSM-Id: 176524
View PSSM: cd08582
Aligned: 22 rows
Threshold Bit Score: 232.205
Threshold Setting Gi: 224539166
Created: 23-Feb-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
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.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          #                                           #                                
NP_865164    48 IVAHRGASyt--aPENTVSAFNLAWEenADAIEGDFYLSADGEIVCLHDKTTARtapgspslkvaeaTLQQLRKLdvgaw 125 Rhodopirellula b...
NP_602097    23 VIAHRGLSsr--fPELTESAFRAALElpIHGIETDVRLTKCGEVVNVHDPIVDRvsngrg--rvsrlDLESLLSLnfgtk 98  Corynebacterium ...
NP_940557     3 IIAHRGFRgr--yPEMTAQAYEKACElpIHGVECDVRLTADGHLACVHDRTLLRiascgl--vvstaTMDQLREHg---- 74  Corynebacterium ...
EFD50857      5 VIAHRGASaa--fPEHTRAAMLHALAvgADGLECDVQLTRDREVVCWHDPTVDRtsdghg--avadhTLDRLRGLdvvsw 80  Micrococcus lute...
NP_809463    18 VIAHRGYWktagsAQNSITALQKADSihCYGSEFDVWLTKDNKLVINHDPVYKMkymey----skgdALTGLKLSng--- 90  Bacteroides thet...
YP_818102   107 LIAHRGASnl--aPENSIPAFQLAKG--SYGAETDIWLTKDKQWVVSHDGTIDRmtnghg--aikdlTLAQIKQYhidsg 180 Leuconostoc mese...
ZP_02417648 210 FVAHRGLSse--aPESTVKAFELAGDagFWGAETDIRMTKDGKFVAVHDTTLKRtcgvdk--rpedmTEAEIRKLkiisg 285 Anaerostipes cac...
ZP_05573733  38 WIAHRGNNte--yPENSIPAFKTVRR--HWGIETDIQVTSDGQWVVMHDDTVDRttngtg--kvssmTLAQFRNLridtg 111 Enterococcus fae...
ZP_04856271 222 YILHRGEQte--aPENSVPAFEMAGRngAEFVETDVRETADGVLVVSHDDSLLRmcgedr--lisemTYEEIKQYpiing 297 Ruminococcus sp....
ZP_03679705 112 VVAHRGAWrqkgvLQNSVRSFQNAVElgCQGSELDVWLTADNRVVLSHDPHVYGle---------veNITSLQLFqqtin 182 Bacteroides cell...
Feature 1                                                                                       
NP_865164   126 kh----------------eryagerIPTLKEVIATVPd---gKGIFIEIK-------CGPEILPILKQQLeecs------ 173 Rhodopirellula b...
NP_602097    99 --------------------etpekVLTLNNLLDIFEdy-pdKHLYIETKhp---mrYAVMLEEEITKILkyrg------ 148 Corynebacterium ...
NP_940557    75 -------------------------IITLDELIDILPe---dKHLYIETKhp---mrYGVMAEEQVALRLryrg------ 117 Corynebacterium ...
EFD50857     81 harrpgaepatttappaayggageqVLTLADLLAIATaadrpLRLAVELKhp---spFGHELEERVLRELlragwdp--- 154 Micrococcus lute...
NP_809463    91 -----------------------enLPSLEQYLEAGKkc--nTKLILELKaln-skkRETKAVQEILALVtkl------- 137 Bacteroides thet...
YP_818102   181 vnv---------------gkyqsltLPTLKEYLTEMSnn--nLRPIIEIKqpa--sqMSDGDVQNLIAAVkna------- 234 Leuconostoc mese...
ZP_02417648 286 ngysk-----------ykndpkankVAFLDEYLDVCKek--gMVPVIEIKme---ytTNGRVADSRMQGVkegdlqklse 349 Anaerostipes cac...
ZP_05573733 112 enls-------------rlsdeektPPTFEEYLKICKel--nKVPVIEIKsg----tYSKANFDLLKDTLdlyg------ 166 Enterococcus fae...
ZP_04856271 298 rna---------------sqypdnlIPTLEQYIACCNky--sVTPVIEIKs-----iRTEEAMNLFMQLLte-------- 347 Ruminococcus sp....
ZP_03679705 183 ---------------------ekdpVPSLQELLIAARaq-nsTHPIIEIKdsqkgleRTLQLTDSVVNIVhrm------- 233 Bacteroides cell...
Feature 1                                                                                       
NP_865164   174 -----lkpEQITIICFNdeVVRQAREMMPy----EANWLTSYKkqltggwkpslvsv----------tdqlkstnasgfg 234 Rhodopirellula b...
NP_602097   149 ----ltedPRIHIISFAlpAMYRMARLAPq---lDRIHLRRSWerwgnpr-----------------------dvrcgvp 198 Corynebacterium ...
NP_940557   118 ----llhdPRFHLISFShaAIRRMGRIAPg---fDTIYLRREWelrynpkd---------------------faisrpsa 169 Corynebacterium ...
EFD50857    155 -etgrvgqVQVSLMSFHpdALRHVAPLAGtdplcPLMDLMPTElptrfargplsraavraaarqslagsealvwrgragl 233 Micrococcus lute...
NP_809463   138 -----gleNRMEYITFSlhAMKEFIRLAPag--tPVFYLNGELspkel---------------------------kdlga 183 Bacteroides thet...
YP_818102   235 -----glyNNSTIISLQceALKHVYALDKki-slELLWDSASDpvqlsek-----------------------lnelgpk 285 Leuconostoc mese...
ZP_02417648 350 tvekkmdgEQYMFIAYDfdTMVEMRKIVKdmpnvKLQHVTNNAdagmi---------------------------nyyyk 402 Anaerostipes cac...
ZP_05573733 167 -----ygeANCVIGSFDanILNTIRTYYPn---iELHYFVDAInesvitq-----------------------ikklgvp 215 Enterococcus fae...
ZP_04856271 348 ------sqKEPVLICFRieTLGKLREMGFt---gKMQWIRTVRmnasmi--------------------------qqckk 392 Ruminococcus sp....
ZP_03679705 234 -----kmqGYVEYISFNyeVLKRIRELDPt---aRTLYLWEGKkelkdl--------------------------vndri 279 Bacteroides cell...
Feature 1                                                                
NP_865164   235 TQVKPELvgsvlNEAFCDAvrdiGCGMHGWTIDDakVAKRLVEl-DFVSITTNRPAY 290 Rhodopirellula baltica SH 1
NP_602097   199 TGLGLSLerakmDPRMIGAk---GLPTYLFTVDKqkDMLWAREq-GVDMLATNYPDR 251 Corynebacterium glutamicum ATCC 13032
NP_940557   170 WGLSLAHak--iRPQLIGRd---GKKTYMWTVNDadDVRWARDn-GVQLLATDYPDV 220 Corynebacterium diphtheriae NCTC 13129
EFD50857    234 AGPSVAYvr--eHLADVKAwlaaGRRLRVWTVDEreDAEFLLAq-GVQELTTNRPED 287 Micrococcus luteus SK58
NP_809463   184 AGLDYHMgvikkHPEWIKEahdlGLKVNVWTVDKaeDMKWLIDq-KVDFITTNEPTV 239 Bacteroides thetaiotaomicron VPI-5482
YP_818102   286 AGLDINGkk--lTSQTIQAlrqqGRRLNVWTISPs-EFPYYIGl-GVDEITTDANSF 338 Leuconostoc mesenteroides subsp. mesent...
ZP_02417648 403 RGIALDCnyetiSDATLKKfldsKVLVNLWTVDNeeKVWDFIGk-KVDYITTNRKFW 458 Anaerostipes caccae DSM 14662
ZP_05573733 216 AAVSCSYsnsslSTANVKAlhmaGFKVGTWTVPEn-SFEGMKKl-GVEYITTNSLSG 270 Enterococcus faecalis JH1
ZP_04856271 393 YDLDISAeykniSMNDINNahqnGIRISVWLCRNe-DMVDIFRkmGADYITYEKWNT 448 Ruminococcus sp. 5_1_39B_FAA
ZP_03679705 280 SGIDYSYyayrqDKNLTQKareaGLLTNVWTVNNaeELQQYYLl-GVDYITTDEPEL 335 Bacteroides cellulosilyticus DSM 14838

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