1O1Z,1DJX,2FJU,1GYM,1AOD,1XX1,1YDY,3KS5,2PZ0,3L12


Conserved Protein Domain Family
PI-PLCc_GDPD_SF

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cd08555: PI-PLCc_GDPD_SF 
Click on image for an interactive view with Cn3D
Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), 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, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases.
Statistics
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PSSM-Id: 176498
View PSSM: cd08555
Aligned: 13 rows
Threshold Bit Score: 98.2766
Threshold Setting Gi: 157829995
Created: 21-Oct-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
catalytic siteactive site
Conserved site includes 2 residues -Click on image for an interactive view with Cn3D
Feature 1:catalytic site [active site]
Evidence:
  • Comment:Phosphoinositide-specific phospholipase C, glycerophosphodiester phosphodiesterases, sphingomyelinases D, and similar proteins hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
  • Comment:Due to replacement of critical catalytic residues, neither Phospholipase C Related but Catalytically Inactive Proteins (PRIP), SHV3, or Neurospora crassa ankyrin repeat protein NUC-2 have PLC or glycerophosphodiester enzymatic activity.
  • Structure:1GYM_A; the catalytic residues in B. cereus phosphatidylinositol-specific phospholipase C are well conserved in all bacterial PI-PLCs.
    View structure with Cn3D
  • Structure:1DJX_B; the catalytic residues in Phosphoinositide-specific phospholipase C-Delta1 from rat
    View structure with Cn3D
  • Citation:PMID 7664726
  • Citation:PMID 8755729
  • Citation:PMID 9048554

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          #                                                     #                      
1O1Z_A       15 VLGHRGYSakyl----------entlEAFMKAIEagaNGVELDVRLskd--gkVVVSHDedlkrlfgldvkird------ 76  Thermotoga maritima
1DJX_B      176 SSSHNTYLledqlt-------gpsstEAYIRALCkgcRCLELDCWDgpn--qePIIYHGytft----------------- 229 Norway rat
2FJU_B      324 NSSHNTYLtagqfs-------glssaEMYRQVLLsgcRCVELDCWKgkppdeePIITHGftmt----------------- 379 human
1GYM_A       29 PGTHDSGTfklqnpik--qvwgmtqeYDFRYQMDhgaRIFDIRGRLtdd--ntIVLHHGply------------------ 86  Bacillus cereus
1AOD_A       36 PGTHDTMSyngditwtltkplaqtqtMSLYQQLEagiRYIDIRAKDn------LNIYHGpif------------------ 91  Listeria monocyt...
ZP_01961322  36 VHSHNDYLq----------------nVPFYTAYSarcASIEADVFLvd---geLYVAHKeneink--------------- 81  Bacteroides cacc...
EEQ63272      3 ILSHRGWWqnene---------kntiLAFQRSFQn-sFGTEMDIRDygg-gghLVISHDmgsk----------------- 54  Helicobacter pul...
1XX1_A        9 NLAHMVNAv-----------------AQIPDFLDlgaNALEADVTFkgs--vpTYTYHGtpcdfgr-------------- 55  Loxosceles laeta
ZP_04853289  39 MVAHAMGGieglt--------ytntyDAFLVNYDqgfRVFEVDLLLsse--grLVARHEwgesftrqlgqedelaadrqg 108 Paenibacillus sp...
1YDY_A       33 VIAHRGASgylp----------ehtlPAKAMAYAqgaDYLEQDLVMtkd--dnLVVLHDhyldrvtdvadrfpdrarkdg 100 Escherichia coli
3KS5_A        5 IASHRGGTlefg----------dstpHGFTATAAxalEEVEFDLHPtad--gaIVVHHDptldattdxtgaivdxtl--- 69  Agrobacterium tu...
2PZ0_A       14 VIAHRGDSknvp----------entiAAFKRAMElgaDGIELDVQLtkd--ghLVVIHDetvdrttngegfvkdftlee- 80  Thermoanaerobact...
3L12_A       20 VIGHRGARgvxp----------entlEGFAFTLAagvRALEFDVVXtad--gvPVVTHNhhlanaxtrdgqghwltgaer 87  Silicibacter pom...
Feature 1                                                                                       
1O1Z_A       77 -------------------------------atvselkeltdgkitTLKEVFENVsd------------dKIINIEIKer 113 Thermotoga maritima
1DJX_B      230 -------------------------------------------skiLFCDVLRAIrdyafk----aspypVILSLENHcs 262 Norway rat
2FJU_B      380 -------------------------------------------tdiFFKEAIEAIaesafk----tspypIILSFENHvd 412 human
1GYM_A       87 -------------------------------------------lyvTLHEFINEAkqflkd----npsetIIMSLKKEye 119 Bacillus cereus
1AOD_A       92 -------------------------------------------lnaSLSGVLETItqflkk----npketIIMRLKDEqn 124 Listeria monocyt...
ZP_01961322  82 ----------------------------------------arklrnLYLNPIREQfemnggs-gypngksFQLLIDLKtd 120 Bacteroides cacc...
EEQ63272     55 -------------------------------------------sspAFESCLALYakn---------nytFPLALNIKad 82  Helicobacter pul...
1XX1_A       56 ----------------------------------------dcirweYFNVFLKTLreyttpgnakyrdgfILFVLDLKtg 95  Loxosceles laeta
ZP_04853289 109 --------------------------avlsyaefkaakiqgvyeplDWDDVLELMeqy----------pdVYIVTDTKqs 152 Paenibacillus sp...
1YDY_A      101 ryyaidftldeikslkftegfdiengkkvqtypgrfpmgksdfrvhTFEEEIEFVqglnh-----stgknIGIYPEIKap 175 Escherichia coli
3KS5_A       70 -----------------------------akvktatirygagshpxTLEELCALYvd-----------shVNFRCEIKpg 109 Agrobacterium tu...
2PZ0_A       81 --------------------------ikkldagikfgekfageripTLYEVFELIgd-----------kdFLVNIEIKsg 123 Thermoanaerobact...
3L12_A       88 qvaextyaei------raldvggldgrtvygrrfpdqafltgihvpRLGELLDLCagyg--------dqaPYLLLELKsd 153 Silicibacter pom...
Feature 1                                                                                       
1O1Z_A      114 -----------eAADAVLEISKkr----------------------------kNLIFSSFdldlldekfkgtkygylid- 153 Thermotoga maritima
1DJX_B      263 ----------leQQRVMARHLRailgpilldqpldg----vttslpspeqlkgKILLKGKklggllpaggengseatdvs 328 Norway rat
2FJU_B      413 s---------prQQAKMAEYCRtifgdmllteplekfplkpgvplpspedlrgKILIKNKknqfsgptssskdtggeaeg 483 human
1GYM_A      120 dmk----gaedsFSSTFEKKYFvdpiflkteg------------niklgdargKIVLLKRysgsnepggynnfyw----- 178 Bacillus cereus
1AOD_A      125 s--------ndsFDYRIQPLINiykdyfyttprtd-----tsnkiptlkdvrgKILLLSEnhtkkplvins--------- 182 Listeria monocyt...
ZP_01961322 121 yk------etmkVLEQQLLEYRdcfdvk-------------------knplavRVVVSGFlpspeefsnyadfiffdgrp 175 Bacteroides cacc...
EEQ63272     83 g--------lqiPLKKLLTQYNvq----------------------------nYFVFDMSipdallyldmgfkvf----- 121 Helicobacter pul...
1XX1_A       96 slsn---dqvrpAGENVAKELLqnywnng------------------nnggraYVVLSLPdighyefvrgfkevlkkegh 154 Loxosceles laeta
ZP_04853289 153 spd-----eiqqIFTQIVDEAKakdp-----------------------ellkRVVPQIYnremlepvqsiypfds---- 200 Paenibacillus sp...
1YDY_A      176 wfhh---qegkdIAAKTLEVLKkygyt----------------------gkddKVYLQCFdadelkriknelepkmgmel 230 Escherichia coli
3KS5_A      110 vdg----lpyegFVALVIAGLErhs-------------------------xleRTTFSSFllasxdelwkattrprlwlv 160 Agrobacterium tu...
2PZ0_A      124 iv------lypgIEEKLIKAIKeyn-------------------------feeRVIISSFnhyslrdvkkmaphlkigl- 171 Thermoanaerobact...
3L12_A      154 palxhdhaaraeXVAAVLADVRryr-------------------------xepRTVXHSFdwallgecrrqapdlptsyl 208 Silicibacter pom...
Feature 1                                                                                       
1O1Z_A      154 -----------------------------------------------------------------eenygsienfverve 168 Thermotoga maritima
1DJX_B      329 deveaaemedeavrsqvqh--------------------------kpkedklklvpelsdmiiycksvhfggfsspgtsg 382 Norway rat
2FJU_B      484 ssppsapavwageegteleeeeveeeeeeesgnldeeeikkmqsdegtaglevtayeemsslvnyiqptkfvsfefsaqk 563 human
1GYM_A      179 ----------------------------------------------------------------------pdnetftttv 188 Bacillus cereus
1AOD_A      183 --------------------------------------------------------------------------rkfgmq 188 Listeria monocyt...
ZP_01961322 176 rf-------------------------------------------------------------iytpeqslripmmstsf 194 Bacteroides cacc...
EEQ63272    122 ----------------------------------------------------------------------trqseyeinp 131 Helicobacter pul...
1XX1_A      155 edllekvgy-----------------------------------------------dfsgpylpslptldatheaykkag 187 Loxosceles laeta
ZP_04853289 201 ---------------------------------------------------------------------viftlyqthdt 211 Paenibacillus sp...
1YDY_A      231 nlvqliaytdwn----------------------------------------etqqkqpdgswvnynydwmfkpgamkqv 270 Escherichia coli
3KS5_A      161 s--------------------------------------------------------------psvlqqlgpgavietai 178 Agrobacterium tu...
2PZ0_A      172 ------------------------------------------------------------------lyqcglvepwhmal 185 Thermoanaerobact...
3L12_A      209 sqlpenadd----------------------------------------------pgedsakpvgpdydrxteslpqava 242 Silicibacter pom...
Feature 1                                                                                       
1O1Z_A      169 kerpYSLHVPYqafe-------leyaVEVLRSFrk---kgIVIFVWTlnd-----------------peIYRKIRRe--- 218 Thermotoga maritima
1DJX_B      383 qafyEMASFSEsralr-----llqesGNGFVRHnv----sCLSRIYPagwrt------------dssnySPVEMWNgg-- 439 Norway rat
2FJU_B      564 nrsyVISSFTElkayd-----llskaSVQFVDYnk----rQMSRIYPkgtrm------------dssnyMPQMFWNag-- 620 human
1GYM_A      189 nqnaNVTVQDKykvsyde-kvksikdTMDETMNnse-dlnHLYINFTslssggtawnspyyyasyinpeIANYIKQknp- 265 Bacillus cereus
1AOD_A      189 fgapNQVIQDDyngpsvktkfkeivqTAYQASKad----nKLFLNHIsatsltftpr---qyaaalnnkVEQFVLNltse 261 Listeria monocyt...
ZP_01961322 195 rtltQWNGLGRmvetd------ynkvKAFIDKAha---egKAARFWGcpd----------------tktAWNTFMKlg-- 247 Bacteroides cacc...
EEQ63272    132 sfydKACGVWLdefhs------hfidEALILEHlkn--gkAVCIVSPelhkrdyq-------neweeykIIDQKLKen-- 194 Helicobacter pul...
1XX1_A      188 vdghIWLSDGLtnfspl---gdmarlKEAIKSRdsangfiNKIYYWSvdk-----------------vsTTKAALDvg-- 245 Loxosceles laeta
ZP_04853289 212 ddevVAFAADKhlaavtm--sdtranAQLIQELnr---igVPSYIHTind-----------------lkTIAKFKRmg-- 267 Paenibacillus sp...
1YDY_A      271 aeyaDGIGPDYhmlieetsqpgniklTGMVQDAqq---nkLVVHPYTvrsdklpe-------ytpdvnqLYDALYNka-- 338 Escherichia coli
3KS5_A      179 ahsiHEIGVHIdt-----------adAGLXAQVqa---agLDFGCWAaht-----------------psQITKALDlg-- 225 Agrobacterium tu...
2PZ0_A      186 rmeaYSLHPFYfn-----------iiPELVEGCkk---ngVKLFPWTvdr-----------------keDMERMIKag-- 232 Thermoanaerobact...
3L12_A      243 saggQLWCPYFld-----------vtPELVAEAhd---lgLIVLTWTvne-----------------peDIRRXATtg-- 289 Silicibacter pom...
Feature 1                   
1O1Z_A      219 ----iDGVITDE 226 Thermotoga maritima
1DJX_B      440 ----cQIVALNF 447 Norway rat
2FJU_B      621 ----cQMVALNF 628 human
1GYM_A      266 --arvGWVIQDY 275 Bacillus cereus
1AOD_A      262 kvrglGILIMDF 273 Listeria monocytogenes
ZP_01961322 248 ----lDYLNTDH 255 Bacteroides caccae ATCC 43185
EEQ63272    195 ---dkLMLCTDY 203 Helicobacter pullorum MIT 98-5489
1XX1_A      246 ----vDGIMTNY 253 Loxosceles laeta
ZP_04853289 268 ----aYGFYTDF 275 Paenibacillus sp. D14
1YDY_A      339 ---gvNGLFTDF 347 Escherichia coli
3KS5_A      226 ----vKVFTTDR 233 Agrobacterium tumefaciens str. C58
2PZ0_A      233 ----vDGIITDD 240 Thermoanaerobacter tengcongensis MB4
3L12_A      290 ----vDGIVTDY 297 Silicibacter pomeroyi

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