Conserved Protein Domain Family
GDPD_GDE5
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cd08607: GDPD_GDE5 
Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative mammalian GDE5 and similar proteins. Mammalian GDE5 is widely expressed in mammalian tissues, with highest expression in the spinal chord. Although its biological function remains unclear, mammalian GDE5 shows higher sequence homology to fungal and plant glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46) than to other bacterial and mammalian GP-GDEs. It may also hydrolyze glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. In addition to C-terminal GDPD domain, all members in this subfamily have a starch binding domain (CBM20) in the N-terminus, which suggests these proteins may play a distinct role in glycerol metabolism.
Links
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Statistics
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PSSM-Id: 176549
Aligned: 15 rows
Threshold Bit Score: 412.458
Created: 22-Jan-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
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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.
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1            #                                                       #                   
Q9NPB8       319 LDVGHRGAGNSTttaq------lakvQENTIASLRNAASHGAAFVEFDVHLSKDFVPVVYHDLTCcltmkkk-------- 384 human
Q10003       402 LEVGHRGAGNSYtkf--------amaRENTIHSLNTAAKNGADYVEFDVQLTKDRIAVIYHDFHVlvsvarrdglampp- 472 nematode
XP_002609432 359 LDVGHRGMGNSYtaas------vahiRENTIASFLSAANHGAAFVEFDVQLTKDKVPIVYHDYKTcistktk-------- 424 Florida lancelet
NP_608804    371 LDVGHRGSGTSFkakd-------aviRENTITSLKNAAEHGADMVEFDVQLSKDLVPVVYHDFMIyvslksk-------- 435 fruit fly
NP_001024784 412 LQIGHRGMGSSYtkn--------igqRENTIFSLNEAARRGADYVEMDVQLTKDLKTVVYHDFHVlvavagrdsps---- 479 nematode
XP_002119819 284 VHIGHRGSGNSFtskl------ianvPENTVASFKQANENRAQLVEFDVHLTKDMIPIVYHDLTTsckvktk-------- 349 Ciona intestinalis
NP_788526    454 LDVGHRGNGKSYiada-------paeRENTIASFLSAHEHHADMIELDVHLTADGVPVIYHDFGLrtappgk-------- 518 fruit fly
XP_002578737 229 VDIGHRGMGTSFfqpeekqykklpttRENTLDSFRTAVQHGADFVEMDVQLTKDHHVVVYHDFDAvviskkk-------- 300 Schistosoma man...
NP_650171    368 MNIGHKGSGNTYrlgs-------dvvRENTLYGFKQAVLANADMVEMDVQLTQDAQVVVYHDFVLrfmlqrmpsfedlle 440 fruit fly
XP_001989336 364 LDIGHRGTGNTYrlaa-------nvhRENTLYAFKQAALHDAHLVELDVHLTQDAQVVVHHDHVLrfslasaacaeklld 436 Drosophila grim...

Feature 1                                                                                        
Q9NPB8       385 ---------------------fdadpveLFEIPVKELTFDQLQLLKLTHvtalkskdrkes-----vvqeensfsenqPF 438 human
Q10003       473 ---------------pmtreqldssnldYHELPVKDLKLSQLKLLMLDHlsfpqkkenvkk-----lveageeeedfkPF 532 nematode
XP_002609432 425 ---------------------gvtggsqLMEIAVMELTLEDVQSLKLDHktakklpaekea------siddeeppdlhPF 477 Florida lancelet
NP_608804    436 ---------------------cslqehdFLALPMRELSLEQLKKLKVYHiaeglsretrs--------fhnddclehqPF 486 fruit fly
NP_001024784 480 -----------------stptaagenksLHEIAIKDLTLAQLNLLHFEHisrangssaespvalsvtpsktetdelhvPF 542 nematode
XP_002119819 350 ----------------------eepgdvLLEMPVFHFTLKELQSLDMKHrsritntrkld-------fneqdtspdmqMF 400 Ciona intestinalis
NP_788526    519 ---------------------qisrpdqLEYVLIKDINYELLKRLRIFSviagqvreyps--------hnaeprmehrIF 569 fruit fly
XP_002578737 301 ----------------------rggqlcYLRVATKDLNYNELRELNVRHssvlkeshthek-----mneedldpvelqPF 353 Schistosoma man...
NP_650171    441 nqdlli-fayenlnklmllamggskrkdLIAVPLEAFSYDQLKEVKVLRfagskgcdks----------cdrmlleqrPF 509 fruit fly
XP_001989336 437 ddydvwifphehlnrlqllamggvkrgqHLVVPLEAFTYEQLRLAQPLRfaasnsdacg----------tdcdltdqlPF 506 Drosophila grim...

Feature 1                                                                                        
Q9NPB8       439 PSLKMVLESLPe--DVGFNIEIKWIcqqrDGMWDGNls-tyFDMNLFLDIILKTVLenSGKRRIVFSSFDADICTMVRQK 515 human
Q10003       533 PTLLEALTKVDp--DVGFNVEVKYPmmqnNGEHECDh---yFERNLFVDVILADVMkhAGNRRIMFSSFDPDICSMVATK 607 nematode
XP_002609432 478 PTLRKVCSTLPe--HVNLNIEVKFPllqqDGAWEEEmd-tyFDRNEIVDIIMREVLenGGKRRILLSSFDADCCVLLRRK 554 Florida lancelet
NP_608804    487 PQLCDVLDALDv--HVGFNIEIKWSqrleDGKMEEEfe-hvVDRNLYIDCILDVILrkAGNRRIVLSCFDPDICTILRFK 563 fruit fly
NP_001024784 543 PSLAQVLRHVDe--NVGLNIEIKYPmymqDGSHECQg---yFEQNKFVDIILAEVAehAGNRRIIFSCFEPDICTMITKK 617 nematode
XP_002119819 401 PTLKTVLTDVPv--ETGFDIEVKWPtldiNNEFEDGle-syIDANVFVDTILKAVYesAGSRRIMFSSFDIDICILLKRK 477 Ciona intestinalis
NP_788526    570 PTLVEVLEKLPk--SLGIDVEIKWPqrrqGGGSEAEq---tIDKNFFADKVIHQVIqkGCGRPIIFSSFDADMCTMLRFK 644 fruit fly
XP_002578737 354 PLLHSCFEEIDp--DLGFVIEVKYPmelkDGSSEMDh---fFEYNFYVDTILREILthAGKRRILLSCFDPNVCVMLQLK 428 Schistosoma man...
NP_650171    510 PLLLDLLDEENlpvDMGFLIEIKWPqmtnMRRWESGsfkptFDRNFYVDTILEIVLnkAGKRRIVFCSFDADICAMVRFK 589 fruit fly
XP_001989336 507 PLLSDVFSHELs-dKLGICIELKWPqqvsRRRWEGDgfrptFDRNFYVDTILEIVFrlAGKRRIIFASFDADICVMLRYK 585 Drosophila grim...

Feature 1                                                                                        
Q9NPB8       516 QNkYPILFLTQGkseiypELMDLRSRTTPIAMSFAqfeNLLGINVHTEDLLrnPSYIQEAKA--KGLVIFCWGDdtNDPE 593 human
Q10003       608 QNkYPVLFLCVGetqrytPFQDQRTSTSMTAVNFAagaDLLGVNFNSEDLLkdPMPVKKANE--FGMVTFVWGEdlDKKE 685 nematode
XP_002609432 555 QNkYPVLFLSQGvterweEMMDVRCRTVPMAMNFTlaeGLLGVDIHAEDILrnPSFVEEIAK--LKLVCFVWGEdiNDPA 632 Florida lancelet
NP_608804    564 QNrYPVMFLTLGrttkyqKYMDPRGNSMELAVWHAvamEFLGVVAHTEDLLrdPSQVNLAKE--RGLVLFCWGDdnNSKD 641 fruit fly
NP_001024784 618 QHkYPVSFLVVGatnrymPFQDIRSDCSKIAANFAagcELLGVNFHSEELLidQKPIEIAEK--YGLIKFVWGDdlNSKE 695 nematode
XP_002119819 478 QGkYPVFLLTNGdtnfytPLLDPRERTNGMAVGSClaeQFLGVITLDKDVYqtPEVIKKIKS--AGVVFGCYGD--EVTD 553 Ciona intestinalis
NP_788526    645 QNvFPVMFLTQGetkkwqPFLDLRTRTFIAAVNNAqafELAGTAPHAEDFLgeNASEMLRKAkdLGQIAVIWGDdcNSKE 724 fruit fly
XP_002578737 429 QQiYPVFQLGISp-----EYADTRHADFQSLFWSAlshQLLGVCLESDRLLkvPGIIELAHS--HKLVVLAWGEavNIPE 501 Schistosoma man...
NP_650171    590 QNvYPVTLLLEDphs-pvQYADQRVSVQDVAVRFCnslEFLGLTLHANSLLnkPSTMAYLHQ--INLDAFVYGSstIDLE 666 fruit fly
XP_001989336 586 QNlYPVTLLLLHaeq-pvQFLDQRVSIFENAANFAyimEFFGLNLHSGWLLkqPLSLGLIKD--LRMQLICWGPdnNDEL 662 Drosophila grim...

Feature 1                           
Q9NPB8       594 NRRKLKEl-GVNGLIYDRI 611 human
Q10003       686 NINYFKKelGVDGVIYDRI 704 nematode
XP_002609432 633 NMSQLRSm-EVDGIIYDRM 650 Florida lancelet
NP_608804    642 TIKLLKEl-GLHAIIYDKM 659 fruit fly
NP_001024784 696 VQKHFRDemNVDGLIFDRI 714 nematode
XP_002119819 554 NLPMMKQl-NVDIAIYDRI 571 Ciona intestinalis
NP_788526    725 RVQYFTRi-GATATCYDRS 742 fruit fly
XP_002578737 502 KRILLAQs-GVDGIIYDCV 519 Schistosoma mansoni
NP_650171    667 IRNKLKKh-GVLGIIYDRL 684 fruit fly
XP_001989336 663 VRSKLKRy-GVVAVVYDRI 680 Drosophila grimshawi

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