Conserved Protein Domain Family
GDPD_cytoplasmic_ScUgpQ2_like

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cd08561: GDPD_cytoplasmic_ScUgpQ2_like 
Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded by gene ulpQ2 (SCO1419) in the Streptomyces coelicolor genome. It is distantly related to the Escherichia coli cytoplasmic phosphodiesterases UgpQ that catalyzes the hydrolysis of glycerophosphodiesters at the inner side of the cytoplasmic membrane to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Statistics
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PSSM-Id: 176504
View PSSM: cd08561
Aligned: 29 rows
Threshold Bit Score: 236
Threshold Setting Gi: 147830794
Created: 27-Oct-2009
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           #                                            #                               
NP_625701     17 AFAHRGGAad--gLENTLRQFRRAVGAGy-RYIETDVHATRDGKLVAFHDgtLDRVTDGAGRIADLPWENVRHARVAge- 92  Streptomyces co...
ZP_01224549   40 NIAHGTARel--lPGNTLEGALNAVAVGa-DIIELDIHLTADNVVVVRHDasVDLTTNGSGLIADMTLIELQAFDVGfhe 116 gamma proteobac...
ZP_02094365   47 IFAHRGSShl--fPENTELAFLKSFELGv-DAFETDIRLTKDGRIVTQHNedIDETTDGTGKVIDYAYDELKEFNFGykf 123 Parvimonas micr...
ZP_02061956   13 VIAHRGGAgl--wPENTLFALQKAATLGa-DLSEIDIHMSRDGVLVAIHDetVDRTTDAKGLVKELTLAELKKLDAGyrw 89  Rickettsiella g...
ZP_01113078   37 VIAHQGGNle--wPDSTRLAYDEAVEAGa-DVLEMDVHLTLDGHVVVMHDelVDRTTNGHGAIRNMTLAHLKTLDAAyww 113 Reinekea sp. ME...
EFA75485      16 VMAHRGSRyl--mPENTILAFKTALDIGt-DVLETDVRATKDGHLVVFHDkqIVRTTGLPGEVETLTLAQLQEIDAAamf 92  Polysphondylium...
ZP_06361687   57 VIAHQGGEhl--aPSNTLVAFDQAVNLGv-DAIEFDIHMTKDGHLVAIHDptVDRTTDGKGKVNDMTLEEVIALDAGyyf 133 Bacillus cellul...
YP_003270977  45 VIAHADDTgaglwPGNTMPFLEGSAELGv-DVLEMDVHATRDGVLVLMHDesVDRTTDGRGLVRELSLAELEVLEVAhhw 123 Haliangium ochr...
EFC47721      26 ISSHRGSRfi--aPENTLQGFKAMLALGt-GVIEFDVRLTKDHQLVVYHDevVNRTTDHKGPVSSFTVSELKSMKAAyni 102 Naegleria gruberi
ZP_01624957  185 NIAHGAGQge--rPDFTSVAYEYLQTLGphIIFEADINGTADNIPIVMHDstLDRKTDFNEINCPDKLPAPEDKHFThnd 262 marine gamma pr...
Feature 1                                                                                        
NP_625701     93 -----------------------------------epVPLFEELLETFPa----------VRWNVDVKae---------- 117 Streptomyces co...
ZP_01224549  117 idype------------------------kqavdgirVPTLESLFEALPd----------RRFLIELKpns--------- 153 gamma proteobac...
ZP_02094365  124 kdingdfp-------------------yaenrvnglyPMEVSALFEKFRd---------dVVYSIDIKddge-------- 167 Parvimonas micr...
ZP_02061956   90 tndegrt---------------------fpfrgqgikIPSLNEIFSAFPn----------ESIMIEVKqng--------- 129 Rickettsiella g...
ZP_01113078  114 pyhdlddvtkta----------vpedavfpfrgqgeqIMTLADMFEAYPn----------HRFVVELKsdr--------- 164 Reinekea sp. ME...
EFA75485      93 spdngtt---------------------rpfrnkgirVPLAREMFDALPp---------aTPLNIEIKedd--------- 133 Polysphondylium...
ZP_06361687  134 ndlnge----------------------ysfrglgirIPTIDEIFTHFSn----------TRMVIEIKdsnrp------e 175 Bacillus cellul...
YP_003270977 124 sqdggas---------------------ypyrghglrVPTLEAVFERFPa----------YPMNIEMKqra--------- 163 Haliangium ochr...
EFC47721     103 kdkkgsf---------------------afrnneeikISTLKEVFEEFWgkypkiltssdVNMNIEIKdnd--------- 152 Naegleria gruberi
ZP_01624957  263 cgriseltfedilsydagyhwtqddgasfpyrdqglsAVSLESLFKRFPd----------AHYVIELKpeendgvgsfiq 332 marine gamma pr...
Feature 1                                                                                        
NP_625701    118 ---pALEPLLELIGRhn---awDRICVGSFSe----aRVVRAQRLag-------prLATSCGTRGVLGLRLrswgv---- 176 Streptomyces co...
ZP_01224549  154 --tdTGVALCQLVLAhg---lqNQVVVGSFYs----sVLRDFRRQcp--------dVPTSLGEEEVQVLVLlswigl--- 213 gamma proteobac...
ZP_02094365  168 vglkSAELLYKFVKEyn---leKNVIFSSFNe----eNLKHLRKIsk-------geIIISGSMQKTTEVVLasyfgy--- 230 Parvimonas micr...
ZP_02061956  130 --ppIIATLRALINGhn---kaKHVLVSAFNs----rTMKVMRKLcp--------hMATAATQVEMECFSKlsqlff--- 189 Rickettsiella g...
ZP_01113078  165 --qtLRSAVLALLERyd---rwDSVLLASFYq----eALQAVRREap--------qAQTYGAEAEIRLFYVlhrlym--- 224 Reinekea sp. ME...
EFA75485     134 --rnVSQLLWSEIERafdngrpHRSIVVSSRfcaptsHIRELAAQyaskhqltelpITTSACEKDVVRFLLlaqfflak- 210 Polysphondylium...
ZP_06361687  176 lyesIVDELWTKINQyd---vqDNVLVASFNq----dIIEMFIDKag-------deVAISGGRSEIKRFVIfhklll--- 238 Bacillus cellul...
YP_003270977 164 --paIAAPLCRLIRRfe---rqDAVLVASFHd----dALDEFRARcp--------eVATSAGPGDTKRFVVadmlgl--- 223 Haliangium ochr...
EFC47721     153 --mlASELLIDLLSKyek--snEHVLIVSNYc----pPLENIQNKlp--------lVPTGTCEKEAMSFVIyhilndlfy 216 Naegleria gruberi
ZP_01624957  333 edlnTGVEVARLINEyr---mkHRVTVASFTd----eIIKDFRLQdd--------dILTAFSEAEALPLMLavfggdd-- 395 marine gamma pr...
Feature 1                                                                                        
NP_625701    177 ----------pvaprRSAVAAQVPEtqs----gvpVVDHRFLRAAHa-rGLQVHVWTVNDadRMHRLLDL-GVDGIMTDH 240 Streptomyces co...
ZP_01224549  214 ----------ghlysASGYSVQLPFeyk----gveLISKSLLRTARe-lNLAVDVWTINDpqQMLELKNL-GVNGIITDR 277 gamma proteobac...
ZP_02094365  231 ----------dsfkkFNTHAMMLPRfek-----lpLDTKYLIYKFHk-hNIAVCYWTINTekDMRKLINK-KVDGIITDR 293 Parvimonas micr...
ZP_02061956  190 ----------trpfsLSAAALEVPYk---------KVTAHLIKAAHk-kNIRVDAWTVNEtkEMERLFAL-EVDGILTDF 248 Rickettsiella g...
ZP_01113078  225 ----------erlfpYDIDAFAIPMqsg----gfdLSTPRFVQAARn-aGILLHYWTINDdaNMQALTAL-GVDGIITDR 288 Reinekea sp. ME...
EFA75485     211 -------iwyswfpiNNYEVFQIPTasg----pmaLDTPRVIDAAHy-fGKHVHYWVINSpgEIDRIASL-GIEGIITDR 277 Polysphondylium...
ZP_06361687  239 ----------nslysPKVDAIQIPIqeg----nfnLKDKKLIRGAHa-rGMDVHYWTINDrtTMEKIIEL-GADGIITDR 302 Bacillus cellul...
YP_003270977 224 ----------talisPEYEAFQVPLsws----ggpLITAARVAAAHa-rGIEVQAWTINDpeVMASLLAM-GIDGILSDR 287 Haliangium ochr...
EFC47721     217 pfveigklfmkdrleNQYSAFQLPTshm----ginFSTPYFVQDAHalnSKEIHYWVVNTkqSMKQLLLL-GAECLITDR 291 Naegleria gruberi
ZP_01624957  396 ---------syevpaPAGEFLQIPEnyslngldlnLVNDSNVNFLLsafDLRVHVWTVNEseAMDRMLDVeNLAGIMTDF 466 marine gamma pr...
Feature 1                
NP_625701    241 IDTLRKVM 248 Streptomyces coelicolor A3(2)
ZP_01224549  278 PDVLHAID 285 gamma proteobacterium HTCC2207
ZP_02094365  294 VDLLLKIK 301 Parvimonas micra ATCC 33270
ZP_02061956  249 PDRMINLL 256 Rickettsiella grylli
ZP_01113078  289 PARLIDLQ 296 Reinekea sp. MED297
EFA75485     278 PDNAVRVL 285 Polysphondylium pallidum PN500
ZP_06361687  303 PDIALDLL 310 Bacillus cellulosilyticus DSM 2522
YP_003270977 288 VDLLSALL 295 Haliangium ochraceum DSM 14365
EFC47721     292 TDLALEVW 299 Naegleria gruberi
ZP_01624957  467 PHALMQKI 474 marine gamma proteobacterium HTCC2080

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