1YDY,2OOG,1T8Q


Conserved Protein Domain Family
GDPD_periplasmic_GlpQ_like

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cd08559: GDPD_periplasmic_GlpQ_like 
Click on image for an interactive view with Cn3D
Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. In E. coli, there are two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the glp operon codes for a periplasmic phosphodiesterase GlpQ. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for GlpQ enzymatic activity. This subfamily also includes some GP-GDEs in higher plants and their eukaryotic homologs, which show very high sequence similarities with bacterial periplasmic GP-GDEs.
Statistics
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PSSM-Id: 176502
View PSSM: cd08559
Aligned: 44 rows
Threshold Bit Score: 262.21
Threshold Setting Gi: 167764301
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:1YDY;The catalytic site of Escherichia coli periplasmic glycerophosphodiester 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

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                   #                                         #                                
1YDY_A              31 KIVIAHRGASGYlPEHTLPAKAMAYAQgADYLEQDLVMTKDDNLVVLHDHYLDRVTDVadrfpdr--------------- 95  Escherich...
NP_833229           38 FLNIAHRGASGHaPEHTFASYDLVKKMkADYLELDIQLTKDGQLIAMHDTAVDRTTNGt--------------------- 96  Bacillus ...
P37965              38 ILTVAHRGASGYvPEHTILSYETAQKMkADFIELDLQMTKDGKLIVMHDEKLDRTTNGm--------------------- 96  Bacillus ...
NP_979008           39 IKNIAHRGASAYaPEHTIAAYTLGQQLkGDYIEIDLQMTKDGYLVAMHDETLNRTTNGt--------------------- 97  Bacillus ...
REF_jgi:Pjdr2_2736  45 AAIIAHRGASGYaPEHTLAAFRSAIEAgADFIEIDLQLTKDGQIVAMHDNTVNRTTNAk--------------------- 103 Paenibaci...
YP_643095           22 VLNVGHRGASGYaPEHTFTAYDLALRMgADYIEQDLQMTRDGVLVVLHDETLDRTARPtaesg----------------- 84  Rubrobact...
EET72077            46 IGVIAHRGASGYaPEHTLTAYKKAIQMkADYIELDLHMTKDGELVAIHDATLSRTTNAeevyp----------------- 108 Geobacill...
ZP_03478729         24 PSIIAHRGTCYWaPEGTEAAMRWARNAgATYLECDLQRTKDGYLVLFHDLRLTRTSDIdskyp----------------- 86  Parabacte...
NP_793241           40 PAAIAHRGASFDaPEETIPAYTLARDLgADYLEMDIQRTKDGVLIALHDDVLERTTNIaqvfp----------------- 102 Pseudomon...
ZP_02436428         57 YAVMAHRGSTFWaPEETESAWRWAREMgADYLESDLQCTKDGVILANHDDNLKRTTNIenvyselvpatrkafymrhgms 136 Bacteroid...
Feature 1                                                                                              
1YDY_A              96 -----------arkdgrYYAIDFTLDEIKSLKFtegfdiengkkvqTYPGRfpm--gksDFRVHTFEEEIEFVQglnhs- 161 Escherich...
NP_833229           97 -----------------GEVRDKTLSEIKSLDAgsw-------fnkAYPEKakq--eyvGQKVPTLEEIFQKYGr----- 145 Bacillus ...
P37965              97 -----------------GWVKDHTLADIKKLDAgsw-------fneAYPEKakp--qyvGLKVPTLEEVLDRFGk----- 145 Bacillus ...
NP_979008           98 -----------------GLVKEHTLEEIKQLNAgst-------ynkKYPNLakk--eyeNAKVPTLEEVIEVFGh----- 146 Bacillus ...
REF_jgi:Pjdr2_2736 104 -----------------GKVGAMTLDVIKQLDAgsw-------fnkHHPMYare--eyaRQQVPSLTDIFTAFGr----- 152 Paenibaci...
YP_643095           85 ------------pgdctGLVREKTLAQIKTCDVgsw-------fneAYPQYarp--eyvGLRIPTLEEVFQRYRk----- 138 Rubrobact...
EET72077           109 -------------grspWRVKDFTLSEIKQLDAgsw-------fndAYPEYakk--qysNEKIPTLQETIDYIKqkd--- 163 Geobacill...
ZP_03478729         87 -------------erknVAISDLTLEELFKLDMgsw-------fnyTYPSNars--sfsKLDILTLEDLTMIAEgyriqr 144 Parabacte...
NP_793241          103 -------------trvkDPVSTFTLAELKQLDAgsw-------fnkAYPDRard--synGLQILTLDEVIDIAEgga--- 157 Pseudomon...
ZP_02436428        137 eaeaeklveadkasfrpYYAMSYMYEELLALDAgsw-------fneTSIEQaresfseqHQYISALEDQIRYAEgkmlkr 209 Bacteroid...
Feature 1                                                                                              
1YDY_A             162 -----------------------------------tgknIGIYPEIKAPwfhhqegkDIAAKTLEVLKKYGYtg------ 200 Escherich...
NP_833229          146 --------------------------------------sMKYYIETKSPdv----ypGMEEKLLALLQKYNLvgqn---- 179 Bacillus ...
P37965             146 --------------------------------------hANYYIETKSPdt----ypGMEEKLIASLQKHKLlgkh---- 179 Bacillus ...
NP_979008          147 --------------------------------------dANYYIETKSPde----ypEMEEKLLEIINHYEIq------- 177 Bacillus ...
REF_jgi:Pjdr2_2736 153 --------------------------------------eTHYILEIKDSty----npGIEEKLLETIYQYRLe------- 183 Paenibaci...
YP_643095          139 --------------------------------------sVNYYIETKSPea----apGMEEELLRLMDEYGLtrpa---- 172 Rubrobact...
EET72077           164 -------------------------------------anAALYIETKAPnv----ypGMEEKLVDILKKNGYlq------ 196 Geobacill...
ZP_03478729        145 dtfqkriykkin----------griitlyepdpadngnrPGIYTETKEPdl----ypGIELDLKKELERLGWyadnvsnl 210 Parabacte...
NP_793241          158 -------------------------------------nkPGLYIETKVPnk----fpGVEADLKKVLAKRGWltqrpaaa 196 Pseudomon...
ZP_02436428        210 dvngeriytvtgtwnpdkprdcltykfeyvddpqdtgnrPGVYIEFKESwln---psDFEKRVYNKLDELGWniitkpcd 286 Bacteroid...
Feature 1                                                                                              
1YDY_A             201 --------------kdDKVYLQCFDADELKRIKNElepkmgmeLNLVQLIAYtdwnetqqkqpdg-----------swvn 255 Escherich...
NP_833229          180 -------------mssSRVMIQSFSKDSLKKIHSMne-----nIPLVQLLWYypnenneivews--------------gi 227 Bacillus ...
P37965             180 -------------skpGQVIIQSFSKESLVKVHQLqp-----nLPTVQLLEAkqma------------------------ 217 Bacillus ...
NP_979008          178 ----------------DKVIIQSFSEESLQKIHNLnv-----nIPLVQLLSYkkav------------------------ 212 Bacillus ...
REF_jgi:Pjdr2_2736 184 ----------------DQVIIQSFDAKSLKKIHRLnd-----rIELLQLMWYntpa------------------------ 218 Paenibaci...
YP_643095          173 -------------aerWQVLIQSFSPASLQKVHALdp-----sLPLIQLFSGtets------------------------ 210 Rubrobact...
EET72077           197 ---------------pGKVIFQSFSAASLRKLREIvp----kgIPLIQLYSPamiqg----------------------- 234 Geobacill...
ZP_03478729        211 ksiktkpghiyiantpARIVVQTFSQASLKKLRQSfp----rlIPMCYLIGIaakdnv---------------------- 264 Parabacte...
NP_793241          197 a------ghvnvahmpGRVVLQTFEKQSLELLQKEmp-----qVPKVLLLWIgegsiepkssvafkdsgakdkasyyaaq 265 Pseudomon...
ZP_02436428        287 gepfyknnkvnvgntnGKVILQTFSLESLRRTAEEfk----gkIPMCFLLWEgngatdlk-------------------- 342 Bacteroid...
Feature 1                                                                                              
1YDY_A             256 ynydwmfkpGAMKQVAE-YADGIGPDYHMLieetsqpgniklTGMVQDAQQnKLVVHPYTVRsdklpeytpdvNQLYDAL 334 Escherich...
NP_833229          228 thepksvtnDDFQEIKK-YAAGIGPNLRNDngel-----iidESYMKMARKnGLLIHPYTINe----------KPDMRLL 291 Bacillus ...
P37965             218 -----smtdAALEEIKT-YAVGAGPDYKALn-----------QENVRMIRShGLLLHPYTVNn----------EADMHRL 270 Bacillus ...
NP_979008          213 -----qlteLEIKKYKT-YCIGLGMNYKYId-----------SAYVKRIKKhGLEVHPFTVDn----------EQDMKKL 265 Bacillus ...
REF_jgi:Pjdr2_2736 219 -----rissVSLNKIKK-YATGISPNFPKIn-----------AAYVHKVQKsGLRIYPYTVNy----------QLNMDRA 271 Paenibaci...
YP_643095          211 -----etirAKLDATAA-YAVGIGPSKDDVd-----------AELVGAAHArCLDVHPYTVNe----------SAEMEGL 263 Rubrobact...
EET72077           235 -----qnldDVLDQAAE-YAEGVGPELSLVt-----------PEFVQKAHErHLIVHPFTINt----------KEEMQKQ 287 Geobacill...
ZP_03478729        265 ---nketyeKWINFAIEqGAVIIGPSIYEKdgllg---dllkPWMYDLIKEkGLLIHAYTFK-----------NREQIIN 327 Parabacte...
NP_793241          266 evkspeefqKWIDWAKAhGAIGTGPSSQLAqggdqsymdlvkPWMNNLTHEkGMVIHPYTVDd----------AADFKRI 335 Pseudomon...
ZP_02436428        343 -hdtpqgyaSFINLGLEyKAHIIGPCIAGApndyp---emnaPWQAYLIKKsGMLNHPYSFDsy-------aqMGKYFGQ 411 Bacteroid...
Feature 1                                        
1YDY_A             335 YNk------------aGVNGLFTDFP 348 Escherichia coli
NP_833229          292 IKw-------------GATGMFTNYP 304 Bacillus cereus ATCC 14579
P37965             271 LDw-------------GVTGVFTNYP 283 Bacillus subtilis
NP_979008          266 LLw-------------GVDGMFTNYP 278 Bacillus cereus ATCC 10987
REF_jgi:Pjdr2_2736 272 LSw-------------GVDGIYTDYP 284 Paenibacillus sp. JDR-2
YP_643095          264 IAt-------------GVDGMFTNFP 276 Rubrobacter xylanophilus DSM 9941
EET72077           288 LSl-------------GVDGMFTNYP 300 Geobacillus sp. Y4.1MC1
ZP_03478729        328 YLd-------------MADGFFTNEA 340 Parabacteroides johnsonii DSM 18315
NP_793241          336 RNd-------------GVDGFFTNRT 348 Pseudomonas syringae pv. tomato str. DC3000
ZP_02436428        412 YNwgntvqydellhgiYGDGLFTNRS 437 Bacteroides stercoris ATCC 43183

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