3KS5


Conserved Protein Domain Family
GDPD_pAtGDE_like

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cd08565: GDPD_pAtGDE_like 
Click on image for an interactive view with Cn3D
Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, 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.
Statistics
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PSSM-Id: 176508
View PSSM: cd08565
Aligned: 9 rows
Threshold Bit Score: 217.657
Threshold Setting Gi: 256805749
Created: 26-Feb-2010
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:3KS5; The catalytic site of Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase consists of two conserved histidine residues, which may 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           #                                         #                                  
3KS5_A         5 IASHRGGTleFGDSTPHGFTATAAXALEEVEFDLHPTaDGAIVVHHDpTLDATTDXTGAIVDXTLAKVKTATIRyga--- 81  Agrobacterium t...
YP_003240895  13 VAAHRGYKsaYPENTLLAFRKALELGVDMLEFDLRLTkDKEVVVIHDaTVQRTTNGAGEVRDYTLAELKGLDAGgwfare 92  Geobacillus sp....
ZP_05496677   16 VAGHRGVGafYPENTLLSIQKALEMNVDMIEFDMNLTkDKVVVIMHDrTVDRTTNGKGYIHDMTLKQIKELDAGgkfgka 95  Clostridium pap...
NP_387070      4 IIGHRGARnlWPENSLTGFRNALRLGVDAIEFDVHLTdSGELLVIHDaALDRTVHATGPVRRLSPAGRLATRLRdtd--- 80  Sinorhizobium m...
YP_002945878   3 IVGHRGARnlWPENSMGGFRRLIALGADAVEFDVQETrDGKAVVIHDpLLDRTTEGTGAVREHDAAEVLATRLRkgqgaq 82  Variovorax para...
ZP_05783957    4 ITGHRGARnlWAENSLTGFAEVVKLGVDAVEFDVHLTdAGELVVIHDaTLERTTHGTGEVRALSPEARAATRLKdst--- 80  Citricella sp. ...
YP_002787323   4 IIGHRGSRhlWPENTLEGFGQLVNSGVEGVEFDVHLTaDDQVIVIHDaTLERTTHSSGPVRTRTLSELQSLRLRdsv--- 80  Deinococcus des...
YP_765406      4 IIGHRGGRnlWPENSLSGFRKLAQMPVDGVEFDIHLTrAGEVLVIHDpTLDRTTDADGLVADLRPGENRTVRLKesd--- 80  Rhizobium legum...
ZP_05535373    7 VSAHRGGSerAEAATWEAYKDALESGAEYVEFDIRRTaDGVLVVYHDpRAGHTGPPLSTLTHAELSERAGYDVPv----- 81  Streptomyces vi...
Feature 1                                                                                        
3KS5_A        82 --------gshPXTLEELCALYvd-shVNFRCEIKpgvdglpyEGFVALVIAGLERHSXleRTTFSSFLlASXDELWka- 151 Agrobacterium t...
YP_003240895  93 ------feglkIPTLTELCELLreypeVLCNVEIKpsp---daQEAADLAMDILNRYGYlpRCVFTCFDaQVLTYIHet- 162 Geobacillus sp....
ZP_05496677   96 ------feglkVPTLREFCELVqpyenILLNAEIKek-----tYETVDLAMEVLKEYGLmhRCVFTCFDaFIAAYMYds- 163 Clostridium pap...
NP_387070     81 ---------esIPTLSDVLGILaardgLHLHVEIKsdetgtpyPGIAARVAAELRRFGVdhRSHLTSFDiSVLEECRlha 151 Sinorhizobium m...
YP_002945878  83 eeqradeadecVPSLAEVLKLFap-trMELHVEIKtdaagelpPGAIARTVQALHDAGVaeRSILTCFVpEVLAQVLahw 161 Variovorax para...
ZP_05783957   81 ---------daIPTLDEVLAVLapadgIDLHVEIKldaqrspyPGITEAVADRLRAHGLeqRAVLTSFDpGILSDCRlha 151 Citricella sp. ...
YP_002787323  81 ---------egLPSLEQVLEVFqn-saLELHIELKtdstgqpyPGLEAQVIGTIAQFGLqqRSVLTSFNhEVLQKVRhld 150 Deinococcus des...
YP_765406     81 --------getIPTLEEVLAVFkd-tsLELHIELKtnadgtpyEGLAAKAAATVDRLDLakRSILTSFHpDALVDIRkva 151 Rhizobium legum...
ZP_05535373   82 -----------VDDVMALIAGR-----LVAHLDLKeig---yeREVIDRAVALLGTDGLv-VTTLEDRSvAAVTRAFp-- 139 Streptomyces vi...
Feature 1                                                                                        
3KS5_A       152 tTRPRLWLVSPSvlqqlgpgav---------ietaiahsiHEIGVHIDta-dAGLXAQVQAa--GLDFGCWAAHt--pSQ 217 Agrobacterium t...
YP_003240895 163 hGQKTQGFPGEKmsgfdfge-------------egtyakmWGIGVEMS----LLTPELVARf-qAQGLLVWSYCpddeQG 224 Geobacillus sp....
ZP_05496677  164 yGVRVQGFPKEKmenfvdge-------------tgtysklFAVGIDMK----IITPERVKEf-eNLGILPWSYCpdtdEL 225 Clostridium pap...
NP_387070    152 pHVARLVSVNADwaarqgglsa---------flpaadglvDIVAIHHEl--mADQWELIRSsvpMERLCVWTLNe--eAG 218 Sinorhizobium m...
YP_002945878 162 pRGRVLASLDHRsaemlggitr--------alaryaalpgCIVAVEKKl--lAATWPQCLAalgSERLGAWVVNe--pDE 229 Variovorax para...
ZP_05783957  152 pQVRRLVSADADwvgrqggleg---------fvaavsdlaEIVALRHDf--lAANWEEVCRlwpRERLCAWTVNd--aET 218 Citricella sp. ...
YP_002787323 151 sSARVLRSVDHStlaqaggfkq--------amiqlealpdLLVAVEQSllkeTLQQFSARFg--ADRLGVWVVNh--dAD 218 Deinococcus des...
YP_765406    152 pHIRTLSSFDSRsverlglmn----------glsllkecsDIIAVEKSl--lAAQWEQITElvpVGRLGAWVPNd--iSD 217 Rhizobium legum...
ZP_05535373  140 -GVRTALSLGRDrrelaparlpgtrlselfparriracgaHGVAVHQRl---ARTNVLREAtrhGLFTMVWTVNd--dTL 213 Streptomyces vi...
Feature 1                              
3KS5_A       218 ITKALDLG-VKVFTTDRPTLAI 238 Agrobacterium tumefaciens str. C58
YP_003240895 225 VRYSLECG-VTGMTCNDPLPAM 245 Geobacillus sp. Y412MC10
ZP_05496677  226 VYESIRCG-ARLMTCNNPLPAL 246 Clostridium papyrosolvens DSM 2782
NP_387070    219 IRRWLERG-IGHLTSDSPDLAL 239 Sinorhizobium meliloti 1021
YP_002945878 230 IAQWLAMP-LRQITTDRPDLAL 250 Variovorax paradoxus S110
ZP_05783957  219 MRAWLDRG-VGHLTTDAPDVAL 239 Citricella sp. SE45
YP_002787323 219 LRYWFRQH-LRQITTDRVDLAL 239 Deinococcus deserti VCD115
YP_765406    218 LEYWLAKP-IRQITTDRPDLAL 238 Rhizobium leguminosarum bv. viciae 3841
ZP_05535373  214 MRAFLAHPrVDVLVTDRPRRAV 235 Streptomyces viridochromogenes DSM 40736

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