1ZCC,3I10


Conserved Protein Domain Family
GDPD_AtGDE_like

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cd08566: GDPD_AtGDE_like 
Click on image for an interactive view with Cn3D
Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (AtGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homolgoues. Members in this family 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. AtGDE exists as a hexamer that is a trimer of dimers, which is unique among current known GDPD family members. However, it remains unclear if the hexamer plays a physiological role in AtGDE enzymatic function.
Statistics
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PSSM-Id: 176509
View PSSM: cd08566
Aligned: 62 rows
Threshold Bit Score: 100.069
Threshold Setting Gi: 13377006
Created: 22-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: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            #                                                          #                
1ZCC_A         3 KIVSHRGANrf-----------------aPENTFAAADLALQQGaDYIELDVRESADGVLYVIHDETLDRTTNGTGPVGH 65  Agrobacterium t...
NP_085711     61 IVIAHRGWWgdhkgpsnscganvsyasgqPENSIDAVIGALHNGfEAVEVDIKMTRDGVPILMHDYTLGRTTDIYQGTGQ 140 Mesorhizobium l...
ZP_04450635   16 LILTHRGMRgg----------------niPENTIKSTQLAYQLGsDLVEVDIARSKDGVYYLFHHNNEKRLLGVENGSLE 79  Catonella morbi...
ZP_01824037   14 LIAAHRGTNgg----------------niLQNTSKAYLNSIRHNaDMFEVDVIRSKDGEFFAFHDGQEPLVFGEKIDIRT 77  Streptococcus p...
YP_001727395  25 LIVAHRGFAha----------------niIENTVESMRVAFKLGaDIVETDTMMTKDGTIFLLHTGTEKRLFGQSFSPEA 88  Leuconostoc cit...
YP_003156158  28 LIITHRGTTlg----------------sfPDNTVRAAVAALRSGtDIVEVDVIRSLDGEYFLFHNGYENKHFASGTDLRT 91  Brachybacterium...
EEF87197     209 SIATHRGAWgdnl------------gaglPENSIAAIAATKKYT-DILESDVMTTKDKRLVISHDYNLKRLSDYSGSDRD 275 Bacteroides cel...
NP_639395     76 VVLAHRGLWgkyag-----------ipdmPENSRGSLQTANDQCmDGVELDVKLTSDGVPVLLHDYNLGRTTTVWQHHPG 144 Xanthomonas cam...
YP_002908706  69 TVLAHRGLWggyla-----------gnnaPENSYTAFAQADSRCmDGIEIDVKMTRDGVPVAMHDFNLGRTTSIWQGARQ 137 Burkholderia gl...
P55427        53 LLSAHRGSWev-----------------yPENSAYALQDAWNSQiEAVEVDARFTADKEVILSHDYRMERESTGTGFLYD 115 Rhizobium sp. N...
Feature 1                                                                                        
1ZCC_A        66 m-----------------------LSSEIDTLDAggwf-----ddrfKGAIVPRLDAYLEHLRGr-------AGVYIELK 110 Agrobacterium t...
NP_085711    141 pkfdpsaqshdqpegynpyvnqidWYGDLEHHYLlspd-----rsrlDSQHIPTFTQLLDSYRSkq----tsGIVVLDVK 211 Mesorhizobium l...
ZP_04450635   80 k----------------------lTSAEIDALAYlngi------gddSGYHLEKLSDFLAWLPAd-------GLVNIDRS 124 Catonella morbi...
ZP_01824037   78 l-----------------------SSEEIQRKECfnsl------nepILQKIEKISDVLKNFEGq-------SLINIDRS 121 Streptococcus p...
YP_001727395  89 i-----------------------TAKQFINKHYynni------gelSSYQPVTLCNFIKQLPRn-------RMIHLDRG 132 Leuconostoc cit...
YP_003156158  92 l-----------------------TAAEIDERSFqwq-------gerGALRPTRLTDLLEALPD--------AWLNIDRS 133 Brachybacterium...
EEF87197     276 ylf-------------------dmNLSQIINLHLrkkn------mevSEYKYLTFEDLVDALVKy------qLVLTVDIK 324 Bacteroides cel...
NP_639395    145 vkydpitnq------gvnpsilvtPWSEVSQLFLltpd-----rrtaTGYHVPRVDELFAYYKQhn----lrTPMVFDIK 209 Xanthomonas cam...
YP_002908706 138 qkydpyknt------gynpsvdsiSSFTLSYARLlspd-----rskiTRESIPTIQKVIDGWIKfk----yrSILVFDTK 202 Burkholderia gl...
P55427       116 q-----------------------NYSQVQQADLrdrhgrvfkdsrgRNAKFMTFSAALDLLAQyvtddghgYVMIIDVK 172 Rhizobium sp. N...
Feature 1                                                                                        
1ZCC_A       111 Yc-----------------------------------DPAKVAALVRHLGm------------vRDTFYFSFSe------ 137 Agrobacterium t...
NP_085711    212 Dr----------------------------------gSMQEVWRLMNNHRdshg------slarNWVAVKFNVstypnpa 251 Mesorhizobium l...
ZP_04450635  125 Wfy---------------------------------wDDPAFMRLFVDTQt------------lDRVFFKSPLed----- 154 Catonella morbi...
ZP_01824037  122 Wf-----------------------------------YWDTFLDKLKTYPs------------lNQVLLKSPVkk----- 149 Streptococcus p...
YP_001727395 133 Ws-----------------------------------HLSELLAVLDHFPnq-----------qQQFVIKIKPka----- 161 Leuconostoc cit...
YP_003156158 134 Wf-----------------------------------YWPELLDLLTEVGa------------vRRLLLKSPP------- 159 Brachybacterium...
EEF87197     325 DvrarynkdgtcmdncdydtkthgdiakkkikdsfmeILRECIRIAMRKNa------------lEYLAFKVNY------- 385 Bacteroides cel...
NP_639395    210 Da-----------------------------------ATVRAVRKAAESQfgv--------asaSYVAAKVNAtl----- 241 Xanthomonas cam...
YP_002908706 203 Ta----------------------------------sAVTAIGKIIKAEGnvtdpgkgsiyqksDYFAMKVNAttf---- 244 Burkholderia gl...
P55427       173 Gavd-------------------------------dqDPTDPIELTQRCL--------------DILAAKKNPkls---- 203 Rhizobium sp. N...
Feature 1                                                                                        
1ZCC_A       138 ---eMRQGLQSi--------------aPEFRRMMTLDIAKSps------------lvGAVHHASIIEITPaq-------- 180 Agrobacterium t...
NP_085711    252 dleaDLFKYADphnd---------nsqEPFLGIPLLTNNMLdkfhnli---eieknyLTKDYTLGMEVNLnmkng----- 314 Mesorhizobium l...
ZP_04450635  155 ---eLLDKLNSh--------------rLDVFYMPILREQMDmsy----------fdaYPYVHCIGAELLPte-------- 199 Catonella morbi...
ZP_01824037  150 ---eLLEMLRDs--------------gLNVMYMPIIKTIEEldf----------vlsFEGINTVAVELVFqdlen----- 197 Streptococcus p...
YP_001727395 162 ---eQIATLRQ----------------HRIKYMTVVIVNHDselqyiln-hltdeinIIGIELVAANLSDs--------- 212 Leuconostoc cit...
YP_003156158 160 ----EAAALTAlaa-----------hpTPFLYYPIVTSPEEfer----------vraVDGLNLIGAEVLAatpd------ 208 Brachybacterium...
EEF87197     386 ----SYQEIREyisa---------dtlAKTLFMPIVHPTRTdyleyi-----dawitQGDKKVVAYQTNFrrtgdrylsp 447 Bacteroides cel...
NP_639395    242 --ytSRDAYRAd--------------gSGMVGIPVFTTNMLgkinvr-----qtisaWMSAGNQTMEINVkqlr------ 294 Xanthomonas cam...
YP_002908706 245 --psYQSFLNAvg-------------gPGLSTAIPVFTPNMltkid------vgsviKNWYSGQVFEIDVknrg------ 297 Burkholderia gl...
P55427       204 --kaVVFKLKAkdavdigtflnrttydPNVMGGLIVVENPDdqnvkdsnydphedtiYDQWNVAPFPVQFemnqfykgdg 281 Rhizobium sp. N...
Feature 1                                                                                        
1ZCC_A       181 -----------mrRPGIIEASRKa----------------------------GLEIMVYYGgd----------------- 204 Agrobacterium t...
NP_085711    315 --------rlqnaYNLVGQSRKPvgifnpiadpgawdgdghnraffmntgqcCYRLWSLAFgdg---------------- 370 Mesorhizobium l...
ZP_04450635  200 -----------enSPLLAADWRSslr------------------------eaGYLVLLNGInigvrhnlfyq-------- 236 Catonella morbi...
ZP_01824037  198 ---------piisKKIIDDLHEK-----------------------------GLLIWVNALtlsdsiilsak-------- 231 Streptococcus p...
YP_001727395 213 -------------HVQLDVIKHIka--------------------------lGLTVMINTLtlntttslfgt-------- 245 Leuconostoc cit...
YP_003156158 209 ---------dpyaDPAAVTSLAEe----------------------------FPLVQVNALnlengarlylg-------- 243 Brachybacterium...
EEF87197     448 fdrggvryqnllhYVYAKTGLRPgiyp---------------------eepaGPKGVANRFgewlmk------------- 493 Bacteroides cel...
NP_639395    295 ----------gllQSDADFIRER-----------------------------GYRVGVFQAipdgpsagkfyqnsgaccy 335 Xanthomonas cam...
YP_002908706 298 ----------gllQNYMNQVRRDy----------------------------YNVGVFNALpdanpskgeffkntgqccy 339 Burkholderia gl...
P55427       282 ---lqayldyvdqKQGFATYHESn---------------------------yYPEGVANSAgkccfehntdpr------- 324 Rhizobium sp. N...
Feature 1                                                 
1ZCC_A       205 -----------------dMAVHREIATs---DVDYINLDRP 225 Agrobacterium tumefaciens
NP_085711    371 ---------------tvdRWDWSFLYGkgwkAFDFITTDEA 396 Mesorhizobium loti MAFF303099
ZP_04450635  237 --------fdedqavlnpSEGWGHIVAh---RPDVIQTDWP 266 Catonella morbi ATCC 51271
ZP_01824037  232 --------idddtaiahdGESWGKLVSi---GFDIIQTDWP 261 Streptococcus pneumoniae SP9-BS68
YP_001727395 246 -------ldddnailaspENIWQEVMIn--yQPNMINTDWA 277 Leuconostoc citreum KM20
YP_003156158 244 -------hddetailedpALGWGPLARs---GATAIQTDWP 274 Brachybacterium faecium DSM 4810
EEF87197     494 ------------daksdmRGDHYFLMSipygKIMVLTTDRP 522 Bacteroides cellulosilyticus DSM 14838
NP_639395    336 alsdlyfsysggrdtadnRGNLDYIVHs--qAFGLITTDDP 374 Xanthomonas campestris pv. campestris str. ATCC 33913
YP_002908706 340 tldsllvvsptlkdtqdlRGDWNYLIDq---GFKTITSDDS 377 Burkholderia glumae BGR1
P55427       325 -------svahggivpdyRGEPEMAIVn---RTNLITTDWP 355 Rhizobium sp. NGR234

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