Conserved Protein Domain Family
GDPD_YPL110cp_fungi

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cd08606: GDPD_YPL110cp_fungi 
Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL110cp and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL110cp and other uncharacterized fungal homologs. The product of S. cerevisiae ORF YPL110c (GDE1), YPL110cp (Gde1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL110cp has been characterized as a cytoplasmic glycerophosphocholine (GPC)-specific phosphodiesterase that selectively hydrolyzes GPC, not glycerophosphoinositol (GPI), to generate choline and glycerolphosphate. YPL110cp has multi-domain architecture, including not only C-terminal GDPD, but also an SPX N-terminal domain along with several ankyrin repeats, which implies that YPL110cp may mediate protein-protein interactions in a variety of proteins and play a role in maintaining cellular phosphate levels. Members in this family are distantly related to S. cerevisiae YPL206cp, which selectively catalyzes the cleavage of phosphatidylglycerol (PG), not glycerophosphoinositol (GPI) or glycerophosphocholine (GPC), to diacylglycerol (DAG) and glycerophosphate, and has been characterized as a PG-specific phospholipase C.
Statistics
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PSSM-Id: 176548
View PSSM: cd08606
Aligned: 6 rows
Threshold Bit Score: 491.961
Threshold Setting Gi: 238493779
Created: 11-Jan-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
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:Based on structure evidence and site-directed mutagenesis of Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase, the catalytic site consists of two conserved histidine residues which serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1               #                                                          #              
Q02979        871 STRVIGHRGLGKNnp-------nkSLQIGENTVESFIMAASL---GASYVEFDVQLTKDNVPVVYHDFLVAETGVDIPMH 940  baker's yeast
Q9C104        746 GVAVIGHRGLGKNqpd------rlSLQLGENTLQSFIKAADL---GASYVELDVQMTKDMVPVVYHDFIVNETGTDAQVH 816  fission yeast
EEH40346      803 SPMVIGHRGLGKNmag------rkSLQLGENTIQSFIAAANL---GASYVEVNVQLTKDHVPVIYHDFLVSETGIDAPVH 873  Paracoccidioi...
XP_002378126  743 GVQLVGHRGLGQNtas------hsYLQIGENTIESFLLASKQ---GATIVESDVQLTRDLVPVIYHDFSLSESGTDIPIH 813  Aspergillus f...
EER25756      714 SVQLVGHRGFGQNtae------rdYLQLGENTVEVGQSCLSAktmGASLVEVNVQVTRDLVPIIYHDFSLSESGTDVPIH 787  Coccidioides ...
XP_504701     541 ATRVIGHRGLGKNtnprgrdelqqQLQMGENTLESFLLASKL---GASHVEFDVQLTKDFQPVIYHDFLVSEAGIDVPMH 617  Yarrowia lipo...
Feature 1                                                                                         
Q02979        941 ELTLEQFLDLNnadkehiqrgaghsphhvngadtalqkyrgrs----vddsdvstlrrawdlhdndpngksnnahwsdnR 1016 baker's yeast
Q9C104        817 SLTLEQFLGAShspseeikddasdiqqkrr------------------------------praysssftpsgsqvnfgeF 866  fission yeast
EEH40346      874 TLTLEQFLHLSeargpresatssnssipvdpvladl------------------rtsaarrqrsmsvgeqfassihmseK 935  Paracoccidioi...
XP_002378126  814 DLNLDQFMHASniqsprgdpvsvlgkanaqpistq--------------------vtstkprsrsltkdhergtreirdR 873  Aspergillus f...
EER25756      788 DVSLNQFLYSGksallddlvrslpndracqr-----------------------------nprsqsltryddkfasanyR 838  Coccidioides ...
XP_504701     618 ALTEEQFSSLHapppkhtdrrkghrgvpkrsesldvgrthrhrafsvsdglervsegdkilegtalqqddpdaddhithR 697  Yarrowia lipo...
Feature 1                                                                                         
Q02979       1017 MRLTKTFKKNNFKGNARGHsIASSFVTLKELFKKIPaNVGFNIECKFPMLDEAEEEELgqIMMEMNHWVDTVLKVVFdn- 1095 baker's yeast
Q9C104        867 AEENARLKPKVYKGNALGHtICAPFTTLKDVLKEVPqSVGLNVEFKYPMLSEAEEEKLlpIAYDYNFYVDTILSIIKky- 945  fission yeast
EEH40346      936 MKHTRDFKKKGFKGNTRGShIQAPFATLEELFRKLPkSVGFNIELKYPMLHESEEEEMdtYAVELNSFVDTVLTSVYdl- 1014 Paracoccidioi...
XP_002378126  874 MKYTVDFVSKGFKPNTRGDfIQDSFTTLEELLEELPeSISFNIEIKYPRLHEAIEAGVapVAIEINTFIDKALERLFsyg 953  Aspergillus f...
EER25756      839 LQHTVDFMKKGFKPNSQGTsIQSPFATLEDLLIKLPkDLGFVIELKYPRPHEAADASVapVAIEVNAFIDVILDKIHrf- 917  Coccidioides ...
XP_504701     698 MKYTRDYKMKGFKGNSRGIsIQAPFTTLREVLQSLPpNVGCNIECKYPMLDEGQAEEMeeFALDLNVWADKVLECVFey- 776  Yarrowia lipo...
Feature 1                                                                                         
Q02979       1096 anGRDIIFSSFHPDICIMLSLKQPv-------------IPILFLTEGGseq--maDLRASSLQNGIRFAkKWNLLGIVSA 1160 baker's yeast
Q9C104        946 ggKRKYIFSSFNPDICILLSLKST--------------NPVLFLTEGGtay--rtDVRAASLRQALKFAsQWSFLGIVSA 1009 fission yeast
EEH40346     1015 gqGRNMIFSSFNPDICLLLSFKQPs-------------IPVMFLTDSGmtn--vgDVRASSLQEAIRFAsRWNLLGVVTA 1079 Paracoccidioi...
XP_002378126  954 nkKRTIILSSFTPEICILLAIKQQt-------------YPVMFITNAGkppvtdrEMRAASIQSAVRFAkRWNLSGLVFA 1020 Aspergillus f...
EER25756      918 gaGRNIVLASFTPEICILLSRKARg-------------YPIMFITNAGkrpitdmEKRGASLQVAIQFArQWNFTGVVLA 984  Coccidioides ...
XP_504701     777 gaNREIIFSSFHPDVCLMLNHKQGgvpmigktevnpvgYPTLFLTESGtap--myDIRASSLQEAIRFCkDWNLLGLVSE 854  Yarrowia lipo...
Feature 1                                                                    
Q02979       1161 AAPILkaPRLVQVVKSNGLVCVTYGVDNNDPENASIQIEAGVDAVIVDSVLAIRRGLTK 1219 baker's yeast
Q9C104       1010 CEPLImcPRLIKAVKQLGLSCYTYGVLNNDVDNVRRQVRFGVDAVIVDNVLAIRRALNQ 1068 fission yeast
EEH40346     1080 AEPLViaPRLVRVVKESGLVCVSYGIANNEPGNVKMQVKEGIDAVIVDSVLAIRKGLTE 1138 Paracoccidioides brasiliensis Pb01
XP_002378126 1021 SEALVmcPRLVRYVQRSGLICGSYGSQNNIPENAKTQAAAGIDIIMADRVGLIAMSLKG 1079 Aspergillus flavus NRRL3357
EER25756      985 AETFLlcPRLIQYVQRSGLLCASYGLVNNVPENAKVQVDAGIDMLIVDRVGLIAKALAS 1043 Coccidioides posadasii C735 delta ...
XP_504701     855 CSPFVmcPRLIQVVKRAGLVCVSYGVLNNNPVIAKTQIKHGVDAVIVDSVKAVHNGLLE 913  Yarrowia lipolytica CLIB122

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