1XX1


Conserved Protein Domain Family
GDPD_like_SMaseD_PLD

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cd08576: GDPD_like_SMaseD_PLD 
Click on image for an interactive view with Cn3D
Glycerophosphodiester phosphodiesterase-like domain of spider venom sphingomyelinases D, bacterial phospholipase D, and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase-like domain (GDPD-like) present in sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.4) from spider venom, the Corynebacterium pseudotuberculosis Phospholipase D (PLD)-like protein from pathogenic bacteria, and the Ajellomyces capsulatus H143 PLD-like protein from ascomycetes. Spider SMases D and bacterial PLD proteins catalyze the Mg2+-dependent hydrolysis of sphingomyelin producing choline and ceramide 1-phosphate (C1P), which possess a number of biological functions, such as regulating cell proliferation and apoptosis, participating in inflammatory responses, and playing a key role in phagocytosis. In the presence of Mg2+, SMases D can function as lysophospholipase D and hydrolyze lysophosphatidylcholine (LPC) to choline and lysophosphatidic acid (LPA), which is a multifunctional phospholipid involved in platelet aggregation, endothelial hyperpermeability, and pro-inflammatory responses. Loxosceles spider venoms' SMases D are the principal toxins responsible for dermonecrosis and complement dependent haemolysis induced by spider venom. Due to amino acid substitutions at the entrance to the active-site pocket, some members lack activity. The typical GDPD domain consists of a TIM barrel and a small insertion domain named as the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. Although proteins in this family contain a non-typical GDPD domain which lacks the GDPD-I, their catalytic mechanisms are based on Mg2+-dependent acid-base reactions similar to GDPD proteins. They might be divergent members of the GDPD family. Moreover, this family does not belong to phospholipase D (PLD) superfamily, since it lacks the conserved HKD sequence motif that characterizes the catalytic center of the PLD superfamily. It belongs to the superfamily of PLC-like phosphodiesterases.
Statistics
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PSSM-Id: 176518
View PSSM: cd08576
Aligned: 22 rows
Threshold Bit Score: 237.989
Threshold Setting Gi: 254384004
Created: 21-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:Spider venom SMase D catalyzes the hydrolysis of sphingomyelin via a Mg2+-dependent acid-base catalytic mechanism which involves two histidines.
  • Structure:1XX1; Loxosceles laeta Sphingomyelinase D catalytic residues.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            #                                     #                                     
1XX1_A         8 WNLAHMVNAVAQIPDFLDLGaNALEADVTFk---gSVPTYTYHGTPCDFg--rDCIRWEYFNVFLKTLREyttpgnakyr 82  Loxosceles laeta
ACN48979       1 FALAHMVNDFDILKSYMDEGaNGIETDITFts--eGEPEKAFHGVPCDCk--rWCRRQVGIDDYLRHLSDlttpgnpkfr 76  Loxosceles aff....
ZP_04999350   47 YAIAHRVDTLAGVDAALKHGaNSIEIDVCAww--nPNEWRAYHDCSSAGdnrlGPSFDSMIDRILSNANAgr-------- 116 Streptomyces sp...
XP_002382643  30 YAIAHRVLRNEAVTAALSHGaNALEVDLTAw----YFGWWADHDGKLFSa---GSTARDLFKFIAQKQWTkdy------- 95  Aspergillus fla...
XP_001819969  38 YAIAHRVLRTEAVTAAISHGaNALEVDLHG-----TDEWWADHDCKKNSa---GDTARELFQFIAEERRNga-------- 101 Aspergillus ory...
XP_001823126 121 FAIAHRVLTIQGMKDAVAHGaNALEIDMRGwsswgRKGWYCDHDGTITSp---GDKAEDMFRAIQDQRRNgk-------- 189 Aspergillus ory...
P20626        40 YAIAHRVLTTQGVDDAVAIGaNALEIDFTAw----GRGWWADHDGIPTSa---GATAEEIFKHIADKRKQga-------- 104 Corynebacterium...
EER25319      72 YAIAHRVLTAQGVRDALKHGaNAIEIDLCAwr--kWNTWLADHDCATGSs--aGDSAVTMFETIVEEHKKgk-------- 139 Coccidioides po...
XP_002584059  48 YAIAHRVVTVGGIKDAISHGaNAFEVDMCAds--iGEGWWANHDCTNGRk--aGDSARKIFETFAAERKRgk-------- 115 Uncinocarpus re...
EEH20034      48 YAIAHMVLDKTGVKDAIKHGaNALEIDVAAy----RGGWWADHDMKAKSk---GWSLESLFQVIAKENKHi--------- 111 Paracoccidioide...
Feature 1                                                                                        
1XX1_A        83 dgfILFVLDLKTGsls------------------ndqVRPAGENVAKELLQNYwnngnnggRAYVVLSLPdi-----ghY 139 Loxosceles laeta
ACN48979      77 dnlVVVVLDLKLNgls------------------eeaLRNGGLRLADKLAAHYwsgn-rkaRAYFIVSVPkt-----seS 132 Loxosceles aff....
ZP_04999350  117 -rlSLVWLDIKDPnyc------------------gerENRGCSVAGLRDKAQRlta--agiQVLYGFYEYhggntpdvgG 175 Streptomyces sp...
XP_002382643  96 -niSFVWLDIKNPdfcrk---------------grpcSIEALRDLAREILEPAg------iRVLYGFFETa-------eS 146 Aspergillus fla...
XP_001819969 102 -niTFIWLDIKNPdecpq---------------hepcSIQALRDLVRETLEPVg------iRALYGFYQTe-------eS 152 Aspergillus ory...
XP_001823126 190 -tiNFVWLDLKKPdeyk----------------agenAIERLRDLARKYLQPWg------vRVLYGFYRShv------dG 240 Aspergillus ory...
P20626       105 -niTFTWLDIKNPdycrd--------------arsvcSINALRDLARKYLEPAg------vRVLYGFYKTv-------gG 156 Corynebacterium...
EER25319     140 -dvTFVWLDMKNPdycep---------------rlncSIEALRNLARKTLEPEg------iRVLFGFYKAe-------kS 190 Coccidioides po...
XP_002584059 116 -tvTFVWLDFKNPdacvk---------------nqgcSIEAIQQLCRDILEKQg------iRVLYGFYKAe-------dS 166 Uncinocarpus re...
EEH20034     112 ---AFVWLDLKTPdmctgkkcnkkvlqpskckenekcSMKSLQQLTRKYLKPAg------vRVLFGFYKKhh-----arS 177 Paracoccidioide...
Feature 1                                                                                        
1XX1_A       140 EFVRGFKEVLKKeghe----dllEKVGYDFSgpylpslptldaTHEAYKkagvdghIWLSDGLTNFspl---gdMARLKE 212 Loxosceles laeta
ACN48979     133 EFMKSFRKELDEinfg----emsAKIGFDFTdnge-----fsgTQKVYEtlgidehIWASDGITNCipll-frgISRLED 202 Loxosceles aff....
ZP_04999350  176 RGWQSLEGRLGSlegit-stgtrDQVQGAFNrsgs----gfpaGRRAMDyg----dSDITKGFGNCteat-yntCAELKK 245 Streptomyces sp...
XP_002382643 147 RGFKVIRDGLNSneavv-lsgetSTILHLYNi-----------SGAGIPv------KQMVMDFGDSwlrkgvdiYPELRY 208 Aspergillus fla...
XP_001819969 153 QGYKEILHSLNEneaislsgsarDVFEMYFTtsrs-----lpvKQRIMDhg----dVNIQKNFGDCherg-gttCSELRN 222 Aspergillus ory...
XP_001823126 241 RAFGVIRDNHNYleavs-indkaANVHKSFQhyga----kiqnTKRVADyg----yFNLGFQFGNCseld-yytCTELRH 310 Aspergillus ory...
P20626       157 PAWKTITADLRDgeava-lsgpaQDVLNDFArsen----kiltKQKIADyg----yYNINQGFGNCygtw-nrtCDQLRK 226 Corynebacterium...
EER25319     191 RALKVIREKLNPyeavs-lsgkaSAVLKEYEgkvas---gipvAQRVMDyg----yYNLRFEFGGChegg-yytCTELRQ 261 Coccidioides po...
XP_002584059 167 RAFKTIRNNLNDreais-lngatTKVLKLFEgtap----kvskHQRVMDyg----dTYLDKGFGDCtekd-wytCTELRQ 236 Uncinocarpus re...
EEH20034     178 AAFDYIQKSLGDgeavc-lsgeaNKVMEIFKkegs----kikpQRRVMDyg----rTELPNGFGDCnekg-gktCAELKN 247 Paracoccidioide...
Feature 1                                                                                        
1XX1_A       213 AIKSRDsa-ngFINKIYYWSVDKv--sTTKAALDVGv-DGIMTNYp--------------nVLIGVLKESgyndkYRLAT 274 Loxosceles laeta
ACN48979     203 LIHQRDepgykYISKVYAWTYDKe--sSVTLALSLGv-DGVMTNYa--------------dFVIGILNKPehsskYRLAT 265 Loxosceles aff....
ZP_04999350  246 GAGDRDa---gRLAATLSWTTTYndpwYVDKLLGDGrvDGIIAGYgaftgvreyddswqcaNSIGLIRDWv---nRHGGT 319 Streptomyces sp...
XP_002382643 209 GSWKRDh---gKLGKVFSWTSAQgdteMVRYLLREAgiDGLIYGYqtdeyndksgpksalkDIVDFVEAHsd--tHRMAT 283 Aspergillus fla...
XP_001819969 223 GRSARNr---gQLGKIFAWTSTEgdtrYVSDLLSVAqvDGIIYGSqkhdykdeartrnafwDILDFVKANpd--aVRMAT 297 Aspergillus ory...
XP_001823126 311 AGRMRDe---gKFGKVFGWTLAVdqadLANALLGTArvDGLIYGFkvtayrdhedtraavkDIQTWVQKHsv--tHYLAG 385 Aspergillus ory...
P20626       227 SSEARDq---gKLGKTFGWTIATgqdaRVNDLLGKAnvDGLIFGFkithfyrhadtensfkAIKRWVDKHsa--tHHLAT 301 Corynebacterium...
EER25319     262 GAQLRDe---gKLGKVYGWTSSSgqvdLVNQLLGTAgvDGIIYGFemtyyyddvltwraalDILTWVKEHgn--tHRMAT 336 Coccidioides po...
XP_002584059 237 GADLRRk---gKLGKVFAWTSTVnqgrLVDQLLGKAhvDGIIYGFkltdyydhadsraaanDIISWVKRRra--lYYMAT 311 Uncinocarpus re...
EEH20034     248 GAKLRQk---gDLQRVFAWTSHVgegkYVNKLLDKAsvDGIIYGFaktryyhhkdteksskDIIDRVKKSk---sRYMVT 321 Paracoccidioide...
Feature 1              
1XX1_A       275 YDDNPW 280 Loxosceles laeta
ACN48979     266 YEDNPF 271 Loxosceles aff. spinulosa GJB-2008
ZP_04999350  320 HRMAGP 325 Streptomyces sp. Mg1
XP_002382643 284 EDDAPW 289 Aspergillus flavus NRRL3357
XP_001819969 298 ADDAPW 303 Aspergillus oryzae RIB40
XP_001823126 386 QNDSPW 391 Aspergillus oryzae RIB40
P20626       302 VADNPW 307 Corynebacterium pseudotuberculosis
EER25319     337 RADPPW 342 Coccidioides posadasii C735 delta SOWgp
XP_002584059 312 NDNNPW 317 Uncinocarpus reesii 1704
EEH20034     322 GADKLW 327 Paracoccidioides brasiliensis Pb03

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