2OTD


Conserved Protein Domain Family
GDPD_EcUgpQ_like

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cd08562: GDPD_EcUgpQ_like 
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Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), can only be hydrolyzed by UgpQ during transport at the inner side of the cytoplasmic membrane to alcohols and G3P, which is a source of phosphate. In contrast to Ca2+-dependent periplasmic phosphodiesterase GlpQ, cytosolic phosphodiesterase UgpQ requires divalent cations, such as Mg2+, Co2+, or Mn2+, for its enzyme activity.
Statistics
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PSSM-Id: 176505
View PSSM: cd08562
Aligned: 25 rows
Threshold Bit Score: 280.263
Threshold Setting Gi: 241668290
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.
  • 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           #                                          #                                 
2OTD_A         9 IVAHRGGGKLAPENTLAAIDVGAKy-GHKXIEFDAKLSkDGEIFLLHDDNLERTSNGwgvagelnwQDLLRVDAGSWYsk 87  Shigella flexneri
YP_573558     35 AIAHRGLSARAPENTLAAVRAAHAa-GCRWVELDVQLLgDGTPVIWHDAGVRRCSNGrgklrrldiERARQLDVGSWFnp 113 Chromohalobacte...
ZP_01116154    8 LIGHRGLPLLAPENTAASVRCAAEh-RISWIEVDVTMAgDGTLVMMHDLTLSRFGQSdralteltkAELMQVDAGSWHsk 86  Reinekea sp. ME...
ZP_04755868    6 YISHRGANSDAVENTIDAFQIAKSa-GFNWFETDVQMSsDGELFLFHDDTPQRFSSIsenvtnmswSELKAIELIHPVvk 84  Francisella phi...
ZP_01166857    6 IIGHRGAALLAPENTLAGIRCAANc-GTQWIELDVTLLgDGTPVLCHDNQLDRCSNQsgpldyltfNDLPSLDVGSWFdp 84  Neptuniibacter ...
ZP_03922886    3 IFAHRGLNRKAPENTLSAFRLAHEa-GVEWIETDVDILgDGTAVILHDSTLDRTTDRcgsiydltvADLDQISAGAKFgd 81  Mobiluncus curt...
ZP_01898929   27 VMGHRGASSIAPENTLAAFQLAEDn-NVPWIEVDVGMLgDGTVVICHDATLDRCSDHngllcdkivTDLDDIDAGAWFgl 105 Moritella sp. PE36
YP_001728288   8 KIAHRGVSAQAPENTRAAFEKMLPl-DITWLETDIDITsDGQLVLIHDASVNRTSNGngkvnrntlQGLQKLDFGEWFsp 86  Leuconostoc cit...
ZP_03924674    6 IIAHRGMSSLAPENTMAAFAACIDy-GVKSFEFDVDIIgDGSLICIHDDSLDRTTTGkggyynldySAIRKLDAGKWFsd 84  Actinomyces col...
BAG24375       4 VYGHRGLPSKAPENTIASFKAASEveGINWLELDVAITkDEQLIIIHDDYLERTTNMsgeitelnyDEIKDASAGSWFge 83  Staphylococcus ...
Feature 1                                                                                        
2OTD_A        88 af--kgepLPLLSQVAERCRehGXXANIEIKPttgt-----gplTGKXVALAARQLWag---xtPPLLSSFEiDALEAAQ 157 Shigella flexneri
YP_573558    114 df--hderMATLDDMLALLAacDMGLNLELKIsykhd---paalAETVIPRALAALPp-----sRLLVSSFDrNALRSAR 183 Chromohalobacte...
ZP_01116154   87 af--agepLLLFADFLKLADelALNVNLEIKVhpd-------ldTEDQVNAVLRTLNdqplkhsRLLISSFDlSALALLR 157 Reinekea sp. ME...
ZP_04755868   85 s----kakVLALKEYLEWAEhnNVFLNLEIKVsneni--nyqkvLVNKVIGLLGAYPnm---ksKILLSSFSkVVMRELR 155 Francisella phi...
ZP_01166857   85 ew--inepMPHLSDALLLCEslGLGLNLEIKAfdld-----palVARKVFEEISVYWqh---pkKLILSSYDlEVLNHYR 154 Neptuniibacter ...
ZP_03922886   82 stsyrherIPLLTDLLTFLKesHMKCNLEVKSneag-----gamSRRLVDTVLREIQdvs--ptELLISSFNhVFLYQIH 154 Mobiluncus curt...
ZP_01898929  106 df--vgerIPTLVDLILFTNetGMNLNLEIKSgsd------kaaTDRLIDGIIRDINhhwqggqQLLLSSFNyLLLAEVK 177 Moritella sp. PE36
YP_001728288  87 vy--qgqqIVTLDWLIDFINlhQLNVNFELKTdvqge--qqnfyLMRIHKAFLRLNPn-----cQIIVSSFNvPLLKKFH 157 Leuconostoc cit...
ZP_03924674   85 ty--tferIPELASVIELMNksQLDANLEIKPcqggh--vlrekLIQHIAVALRELDpq----rRLVISSFDpELLWMAA 156 Actinomyces col...
BAG24375      84 kf--kdehLPTFDDVVKIANeyNMNLNVELKGitgpnglalsksMVKQVEEQLTNLNqn----qEVLISSFNvVLVKLAE 157 Staphylococcus ...
Feature 1                                                                                        
2OTD_A       158 Qaa---peLPRGLLLDEWRd--------DWRELTARLg--------CVSIHLNHKlLDKARVXQLKDaGLRILVYTVNKP 218 Shigella flexneri
YP_573558    184 RqeadphrLRLGLLYDRLPr--------GWQADAEALl--------ASSVHLDWRkLKPGTVAAVHEaGLQLLCYTANDP 247 Chromohalobacte...
ZP_01116154  158 Qcd---saISLGVLFEDLPa--------DIATVVQDIq--------PQSIHCDQSrLTETQAKAVIG-HWPLYCYTVNDT 217 Reinekea sp. ME...
ZP_04755868  156 Rhk----dFTQGKLFYTTNw-------vRDFEYIDGKlyrnfiknrYIAVIINYScLTHSRVKYLKRkFGKVFVYSVYTD 224 Francisella phi...
ZP_01166857  155 Hld---lfAQIGVLYDHLPe--------LWCLQAQALq--------AVSIHCDCNlITADDASAIKNqGFELYTYTCNDL 215 Neptuniibacter ...
ZP_03922886  155 Qqr---pdLQLACLFTKEC---------LWEDAVSRCeq-----vgATAIHPEDSgLTIEITKRLQDaGLQINVWTVNDP 217 Mobiluncus curt...
ZP_01898929  178 Rra---peISLGCLFKSPLp-------vDWLTSMQYVg--------AEFVHPNDKgLTEPQVKAMTDaGYSVNVWTVNSL 239 Moritella sp. PE36
YP_001728288 158 Alm---pkVATGLLVDGPIt-------dSHLEQAQAVd--------AAYIHPDVSfLTQEQARILMNkGFKLNVWTVNDP 219 Leuconostoc cit...
ZP_03924674  157 Kam---peRNFAALTETNHdeplleqvqMWLDIAATFpet---gatLQAMHVDNEgLTAEAVKMMKDaGYKVRVWTVNDP 230 Actinomyces col...
BAG24375     158 Eim---pqYNRAVIFHTTSfr------eDWRTLLDYCn--------AKIVNTEDAtLTKAKVKMVKEaGYELNVWTVNKP 220 Staphylococcus ...
Feature 1                           
2OTD_A       219 QHAAELLRwgVDCICTDAI 237 Shigella flexneri
YP_573558    248 ATFLPCWEwgVDAVISDDP 266 Chromohalobacter salexigens DSM 3043
ZP_01116154  218 VTFERLLTwgVRGVFCDRA 236 Reinekea sp. MED297
ZP_04755868  225 DEIKQLLEwqVDAIFIDKK 243 Francisella philomiragia subsp. philomiragia ATCC 25015
ZP_01166857  216 HLAAKLFEwgVDGIFTDNP 234 Neptuniibacter caesariensis
ZP_03922886  218 TRARELASwgVDGIFTDIA 236 Mobiluncus curtisii ATCC 43063
ZP_01898929  240 ARANQLYNwgVAGICSDIP 258 Moritella sp. PE36
YP_001728288 220 KTMARLNEwgINAAFTDFP 238 Leuconostoc citreum KM20
ZP_03924674  231 ARAAELAEwgVDAIFTDKA 249 Actinomyces coleocanis DSM 15436
BAG24375     221 ARANQLANwgVDGIFTDNA 239 Staphylococcus saprophyticus subsp. saprophyticus

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