1YDY,2PZ0,3L12,2OOG,2OTD,1ZCC,2O55,3KS5,1O1Z,1VD6


Conserved Protein Domain Family
GDPD

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cd08556: GDPD 
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Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins
The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols are major sources of carbon and phosphate. Its catalytic mechanism is based on the metal ion-dependent acid-base reaction, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). Both, GDPD related proteins and PI-PLCs, belong to the superfamily of PI-PLC-like phosphodiesterases.
Statistics
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PSSM-Id: 176499
View PSSM: cd08556
Aligned: 148 rows
Threshold Bit Score: 65.7476
Threshold Setting Gi: 30581062
Created: 4-Jan-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.
  • Comment:The residues essential for enzyme activities and metal binding are not conserved in glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins (SVLs) or in Neurospora crassa ankyrin repeat protein NUC-2 and homologs.
  • Structure:2PZ0; Based on structure evidence and site-directed mutagenesis of Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase, the catalytic site consists of two conserved histidine residues. They serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
    View structure with Cn3D
  • Structure:1YDY;The catalytic site of Escherichia coli periplasmic glycerophosphodiester phosphodiesterase consists of two conserved histidine residues.
    View structure with Cn3D
  • Citation:PMID 6304089

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1           #                                                 #                          
1YDY_A        33 VIAHRGASgylp--------ehtLPAKAMAYAqgaDYLEQDLVMtkDDNLVVLHDhyldrvtdvadrfpdrarkdgryya 104 Escherichia coli
2PZ0_A        14 VIAHRGDSknvp--------entIAAFKRAMElgaDGIELDVQLtkDGHLVVIHDetvdrttngegfvkdftle------ 79  Thermoanaerobac...
2OTD_A         9 IVAHRGGGklap--------entLAAIDVGAKyghKXIEFDAKLskDGEIFLLHDdnlertsngwgvagelnwq------ 74  Shigella flexneri
1ZCC_A         4 IVSHRGANrfap--------entFAAADLALQqgaDYIELDVREsaDGVLYVIHDetldrttngtgpvghmlss------ 69  Agrobacterium t...
Q9NPB8       320 DVGHRGAGnstttaqlakvqentIASLRNAAShgaAFVEFDVHLskDFVPVVYHDltccltmkkkfdadpvelfeipvke 399 human
YP_003198520   6 VFAHRGARahap--------ensWIALLLAQQsgaHGWETDVRLtrDLIPVLVHDhtlyrtsdwvarrpattgllsrlnf 77  Desulfohalobium...
YP_393744     13 IVAHRGANslsp--------entLNALKKSIGr-aDFIEIDTQLskDGIAIIMHDdtllrttnvsqlsefdskkpyrvcd 83  Sulfurimonas de...
ZP_01916161    3 LWAHRGSGkdsl--------entIKGFEIALNsgfNAVEFDVMLtsDSVPMIHHDwvmgrcarsldpamaatdpl----- 69  Limnobacter sp....
ZP_01725209    9 VFAHRGASayal--------entFKAFEKALElgaDGIELDIQFskEGCPIVYHDpqlsrlvginklvsdctme------ 74  Bacillus sp. B1...
NP_692776      4 IIAHRGASkyap--------entRASFELAHQmnaDGIETDVQLskDGIPILFHDekikrimrrkgflqdytyn------ 69  Oceanobacillus ...
Feature 1                                                                                        
1YDY_A       105 idftldeikslkftegfdiengkkvqtypgrfpmgksdfrVHTFEEEIEFVqglnhstgknIGIYPEIKapwfhh----- 179 Escherichia coli
2PZ0_A        80 ---------------------eikkldagikfgekfagerIPTLYEVFELIgd------kdFLVNIEIKsgiv------- 125 Thermoanaerobac...
2OTD_A        75 ---------------------dllrvdagswyskafkgepLPLLSQVAERCre------hgXXANIEIKpttg------- 120 Shigella flexneri
1ZCC_A        70 ---------------------eidtldaggwfddrfkgaiVPRLDAYLEHLrg-------rAGVYIELKy---------- 111 Agrobacterium t...
Q9NPB8       400 ltfdqlq--llklthvtalkskdrkesvvqeensfsenqpFPSLKMVLESLpe-------dVGFNIEIKwicqqrdgmwd 470 human
YP_003198520  78 sdllgad--fgswfasrdpfgtvaageiddtvlaslaatrVLRLDTALAFAak------hdFLTNIELKdqygv------ 143 Desulfohalobium...
YP_393744     84 ----------------ftfeelkrldygswfytdnskaepLLTLHDALIFIke------nnLFLNLEIKdisya------ 135 Sulfurimonas de...
ZP_01916161   70 --------------------trfdslrvrdlrhyavqgepIPSLAQTIAYClk------hnMRANVELKatsps------ 117 Limnobacter sp....
ZP_01725209   75 ---------------------ellrfklgkpwrrlfssakMPAFDAVLAWAkt------nkLPLNIELKstil------- 120 Bacillus sp. B1...
NP_692776     70 ---------------------elksmdigswfgsnfigetIMSLEEFLIWIqd------kpLQLHLELKnnvi------- 115 Oceanobacillus ...
Feature 1                                                                                        
1YDY_A       180 --qegkdIAAKTLEVLKkygyt---gkddKVYLQCFDadELKRIKnelepkmgmeLNLVQLIAYtdwnetqqkqpdgswv 254 Escherichia coli
2PZ0_A       126 ---lypgIEEKLIKAIKeyn------feeRVIISSFNhySLRDVKkma-----phLKIGLLYQCglvepwh--------- 182 Thermoanaerobac...
2OTD_A       121 ---tgplTGKXVALAARqlwa-----gxtPPLLSSFEidALEAAQqaa-----peLPRGLLLDEwrddwre--------- 178 Shigella flexneri
1ZCC_A       112 ------cDPAKVAALVRhlg------mvrDTFYFSFSeeMRQGLQsia-----peFRRMMTLDIakspslv--------- 165 Agrobacterium t...
Q9NPB8       471 gnlstyfDMNLFLDIILktvle--nsgkrRIVFSSFDadICTMVRqkq-----nkYPILFLTQGkseiypelmdlrs--- 540 human
YP_003198520 144 --fadrtVVNAVLEAVHrsgi-----ppeLVLFSSFRpaYLRLVRdla-----pqMKTALLAVRppprvfg--------- 202 Desulfohalobium...
YP_393744    136 --fsdneVVEKIVKEINdiq------csdRVLVSSFRheYLKIIKtk------lhIPTAALAEDshpkells-------- 193 Sulfurimonas de...
ZP_01916161  118 ---naiaLGQAVKATVEelsldqkqhirkHWVFSSFYhaSLLPLQg---------YDLALLYEQlpdnwvl--------- 176 Limnobacter sp....
ZP_01725209  121 ----dnqNGLKDFLQGLsl--------ptGSHFSSFHyeLLEMVKkhr-----peYETALIATKklkwdll--------- 174 Bacillus sp. B1...
NP_692776    116 ---dylhLEVLTYNLVEryg------lldRTFFSTFStrSVQRLYkin-----rdTNIGWLTSKsrqqlpl--------- 172 Oceanobacillus ...
Feature 1                                                                                        
1YDY_A       255 nynydwmfkpgamkqvaeyaDGIGPDYhmlieetsqpgniklTGMVQDAqqnKLVVHPYTvrsdklpeytpdvnqLYDAL 334 Escherichia coli
2PZ0_A       183 -------------malrmeaYSLHPFYfn-----------iiPELVEGCkknGVKLFPWTvdr----------keDMERM 228 Thermoanaerobac...
2OTD_A       179 -------------ltarlgcVSIHLNHkl-----------ldKARVXQLkdaGLRILVYTvnk----------pqHAAEL 224 Shigella flexneri
1ZCC_A       166 --------------gavhhaSIIEITPaqm----------rrPGIIEASrkaGLEIMVYYggd---------dmaVHREI 212 Agrobacterium t...
Q9NPB8       541 -------rttpiamsfaqfeNLLGINVhted-------llrnPSYIQEAkakGLVIFCWGddtn--------dpeNRRKL 598 human
YP_003198520 203 -------------vlrklgaAAYHPHRdg-----------lsGDLVQQLrgeGFDVHVFTvnt----------aaEAQQW 248 Desulfohalobium...
YP_393744    194 -------------ylrglgvDGYCLNDel-----------vdKKSVEMLreaGFFVGVYTvns----------tlRSHVL 239 Sulfurimonas de...
ZP_01916161  177 -------------hadalqaSAIHLHWsg-----------aePVALRRIhttGRVVRVYTvnd----------aeQAKTL 222 Limnobacter sp....
ZP_01725209  175 --------------adykaaDTVHMHKry-----------ykPRYLEACvtsGKACRFYAidg----------nePFLTN 219 Bacillus sp. B1...
NP_692776    173 -------------fsrslgaTAIHIKHrl-----------lqPKLVQQAkteNMPLRVYTvnk----------pkQLELC 218 Oceanobacillus ...
Feature 1                     
1YDY_A       335 YNkagvNGLFTDF 347 Escherichia coli
2PZ0_A       229 IKag-vDGIITDD 240 Thermoanaerobacter tengcongensis MB4
2OTD_A       225 LRwg-vDCICTDA 236 Shigella flexneri
1ZCC_A       213 ATsd-vDYINLDR 224 Agrobacterium tumefaciens
Q9NPB8       599 KElg-vNGLIYDR 610 human
YP_003198520 249 HAag-aSGIFTDF 260 Desulfohalobium retbaense DSM 5692
YP_393744    240 FEmg-vNFIFSDS 251 Sulfurimonas denitrificans DSM 1251
ZP_01916161  223 QAlg-iKGLFTDR 234 Limnobacter sp. MED105
ZP_01725209  220 PHha-vLGWITDY 231 Bacillus sp. B14905
NP_692776    219 FKyn-cDSVFTDV 230 Oceanobacillus iheyensis HTE831

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