2PZ0


Conserved Protein Domain Family
GDPD_TtGDE_like

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cd08563: GDPD_TtGDE_like 
Click on image for an interactive view with Cn3D
Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show 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. Despite the fact that most of GDPD family members exist as the monomer, TtGDE can function as a dimeric unit. Its catalytic mechanism is based on the general base-acid catalysis, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). A divalent metal cation is required for the enzyme activity of TtGDE.
Statistics
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PSSM-Id: 176506
View PSSM: cd08563
Aligned: 32 rows
Threshold Bit Score: 262.493
Threshold Setting Gi: 144574931
Created: 16-Nov-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:2PZ0; The catalytic site of Thermoanaerobacter tengcongensis 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            #                                         #                                
2PZ0_A       12 TLVIAHRGDSKnvPENTIAAFKRAMElGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGFVKDFTLEEIKKLDAGikfg 91  Thermoanaerobact...
P47535        5 QLLLAHRGYSFiaPENTKLAFDLAFEyCFDGIELDVHLTKDEQLVIIHDETTLRTALVNKEVEFESLVSLKRDDHSaffh 84  Mycoplasma genit...
NP_326094     5 QLLLAHRGYMAiaPENTPLSFELAKLfGFDGVELDVHLTKDQKLVIIHDESTNRTALNDKVIANETLNSLKKDDHGlffk 84  Mycoplasma pulmo...
AAZ43445      4 KYILGHRGYFDkaPENTKLAFDLALKhNFDGVELDIHLTKNNKIVIIHDESILRTTGVDLEVYKNNYEDLKDYNYAfyfk 83  Mycoplasma synov...
NP_757961    12 TKILAHRGYSGiaPENTELAFETAVNfGFDGFEIDVHLTKDNQLVVIHDEDTYRTSLVKKMIKDSTLKELKELDQAaffk 91  Mycoplasma penet...
NP_562793     1 MKVFAHRGFSYkyPENTLLAFKEALKlDIYGIELDVHKSKDGKLVIIHDEDIKRTFKGEGKVKDYTFEELRNFKCNkegf 80  Clostridium perf...
ZP_02428166   1 MIKLGHRGYSSkyPENTMLAFKAAIDgNFDGVETDVQLTKDNRLVLIHDEKIDRTSNGKGYVKDYTYDQLCQFNFNyrfd 80  Clostridium ramo...
ZP_03682905   2 MKRLAHRGYSDlfPENTMSAFEKAAHsSFEGIETDVQMTKDGVLVLLHDDKINRTSDGKGVLRHMTFKEARQYNYNnkmd 81  Catenibacterium ...
ZP_02862328   2 SKICAHRGMLKqkTENTISSFKEAMKyDIDSIELDVHLTKDNKLVVFHDFTLERMCDINEYIGELTYDEIKKIKINne-- 79  Anaerofustis ste...
NP_602691    22 MKIFAHRGASGyaPENTLTAIKKAIEmKADGIEIDIQLTKDGKIVVIHDWKVDRTTTGRGFVYELDFDYIRSLDAGqwyt 101 Fusobacterium nu...
Feature 1                                                                                       
2PZ0_A       92 ekfageRIPTLYEVFELIgdkDFLVNIEIKSGIvlypgIEEKLIKAIKeyn--feERVIISSFNHYSLRDVKKMAphLKI 169 Thermoanaerobact...
P47535       85 lkiqfqSILTLKEFLDLYldkFKLINIEIKTDQkpylgIEKKLVDLVKgygkkaiDKILFSSFNFESLQKVYDLDnsYKK 164 Mycoplasma genit...
NP_326094    85 vkvprqTILTLEEFLDKYldvFEIINVEIKSDVyhypnIENKIFELSLkygqkliDKVIFSSFNFETLKIMKKLNpnFKL 164 Mycoplasma pulmo...
AAZ43445     84 nkvekqSLMLLEDFLDLYfdkFKIINIEIKTDKihylnIEKLLYVLVSeyl-nfeNKIVFSSFNFQSLILLKKINpnLKL 162 Mycoplasma synov...
NP_757961    92 incpkqEILTLKELLDKFlyrISYLNIEIKTDIivypnIEKYLDELVKtyd-dayEKIIFSSFNFNSLKTLHELNpkWTN 170 Mycoplasma penet...
NP_562793    81 ennddcKISLLEDVFNLIkdkDIVLNIEIKNDVidyenIEKDVLDLIKeyn--leRKILISSFNHKALEKVKKLNgdIKL 158 Clostridium perf...
ZP_02428166  81 --gieaKIPLLEELLDYCigkDVILNIEIKTDKiqypnIERMTYMMIKekg--llDRVMFSSFHLESLLNLRELDdsIYL 156 Clostridium ramo...
ZP_03682905  82 ---ieeQIPTLHSLLTLLdstDKLLNIEIKDTVsv--gLEEKLRDIIMkhh--mtDRIYFSSTSLERLLNMRALMpdSYY 154 Catenibacterium ...
ZP_02862328  80 -----dNIPLFEEVLDLFtdtDINLNVELKSSSylyndIEHKTVNMIKdyn--meDYTIFSSFDHRALKNIKEIDktLKV 152 Anaerofustis ste...
NP_602691   102 kdfvgeVVPTLEEVLDVLp-nDMMLNIEIKDTArkhsnIEEKMLEVLKkyp-ekfEDIIVSSFHHDKIKRLQELEpkLKL 179 Fusobacterium nu...
Feature 1                                                                                      
2PZ0_A      170 GLLYQCGLVe---PWHMALRMe--aYSLHPFYfniiPELVEGCKKnGVKLFPWTVDrk-eDMERMIKa-GVDGIITDDP 241 Thermoanaerobacte...
P47535      165 GFLFWTKKQfetiSTARIQKIc---QFLHPWTki-yEKYPQMIKKlNLPLNLWTVNsq-nKFQQFLAdnHVYAQIANKK 238 Mycoplasma genita...
NP_326094   165 AFLFWTKTQlekvSKNQIFEVc---DFLNPWTel-yEKIKDELDKfNLPYLLWTIRsndkYQKFLKDk-KVYAQISNYK 238 Mycoplasma pulmon...
AAZ43445    163 GYLFDSMESllrmEKDLILNTc---NFLHPSWkl-yLKNKKELISyNLPLNLWTIRcf-dKLKMFYKdsDINFLISNKK 236 Mycoplasma synovi...
NP_757961   171 GFLWWTKSQfkavNPEEIKKVc---KYLHPWTei-yKKEKDNYLKlGLPFNLWTIKda-kVYEHYAKdkDVHFLISNYK 244 Mycoplasma penetr...
NP_562793   159 GVLYEKEMPn---ILDIAKSLn--aYAIHPAKslvsEELVEKAHNeGVKVNVYTVNek-eDIDKLKNy-GVDAIFTDQA 230 Clostridium perfr...
ZP_02428166 157 GYLYEDNYQv---NKAKVFEYr--fNGAHPKYtflnEKEINDYLRrGIDVNTWTVDsd-dIKDFLVDe-GVKTIITNKD 228 Clostridium ramos...
ZP_03682905 155 ALIVLRGYKk---CKQQVIDHh--lDGIHSRYsyltHEEIVDLKSrHIKIGAWTIKek-eQYDFFKKe-GIDFIFANGL 226 Catenibacterium m...
ZP_02862328 153 GALYEGFFEn---IINYAKENs--fDAIHPQFlcidENIMDKAREcNIEVNCYTINtl-rEYNYIKNl-NVDTIITNIA 224 Anaerofustis ster...
NP_602691   180 ALLTDSEFIe---IEKYLSTNglksYSYHPEInlisKKDVEILHKnDVKVFVWTVNke-eDLDYLVTl-GVDGVITNYP 253 Fusobacterium nuc...

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