1YDY,1T8Q


Conserved Protein Domain Family
GDPD_EcGlpQ_like

?
cd08600: GDPD_EcGlpQ_like 
Click on image for an interactive view with Cn3D
Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli periplasmic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), GlpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the E. coli glp operon codes for a periplasmic phosphodiesterase GlpQ, which is the prototype of this family. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for the enzymatic activity of GlpQ. This family also includes a surface-exposed lipoprotein, protein D (HPD), from Haemophilus influenza Type b and nontypeable strains, which shows very high sequence similarity with E. coli GlpQ. HPD has been characterized as a human immunoglobulin D-binding protein with glycerophosphodiester phosphodiesterase activity. It can hydrolyze phosphatidylcholine from host membranes to produce free choline on the lipopolysaccharides on the surface of pathogenic bacteria.
Statistics
?
PSSM-Id: 176542
View PSSM: cd08600
Aligned: 12 rows
Threshold Bit Score: 449.919
Threshold Setting Gi: 269120164
Created: 16-Dec-2009
Updated: 2-Oct-2020
Structure
?
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:The catalytic mechanism of glycerophosphodiester phosphodiesterases is based on the metal ion-dependent general acid-base reaction.
  • Structure:1YDY; The catalytic site of Escherichia coli periplasmic glycerophosphodiester phosphodiesterase consists of two conserved histidine residues, which serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
    View structure with Cn3D
  • Citation:PMID 6304089

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1             #                                         #                                
1YDY_A        31 KIVIAHRGASGYLPEHTLPAKAMAYAQgADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADrFPDRARKD-GRYYAIDFTL 109 Escherichia coli
1T8Q_A         9 KIVIAHRGASGYLPEHTLPAKAXAYAQgADYLEQDLVXTKDDNLVVLHDHYLDRVTDVADrFPDRARKD-GRYYAIDFTL 87  Escherichia coli
EAQ42617      28 KVVIAHRGASGYLPEHTLEAKAMAYAMqVDFIEQDLVLSKDDVPIVIHDIYLDYVTNVANkFPDRKRED-NRFYVIDFTY 106 Polaribacter sp...
NP_602708     25 KIIIAHRGASGYLPEHTLESKALAFAQqADYLEQDLAMSKDGKLIVIHDHFLDGLTDVAKkFPNRKRAD-GRYYVIDFTW 103 Fusobacterium n...
Q06282        35 KIIIAHRGASGYLPEHTLESKALAFAQhSDYLEQDLAMTKDGRLVVIHDHFLDGLTDVAKkFPYRHRKD-GRYYVIDFTL 113 Haemophilus inf...
YP_002769765  28 KIVIAHRGASAYLPEHTLPAKAMAYAMgVDYIEQDVVMTKDNKLLIMHDHYLDSVTNVAEvYPDRKRKD-GRYYVIDFTL 106 Brevibacillus b...
AAG24364      33 PLIIAHRGASGYLPEHTLEAKAYAYALgADYLEQDIVLTKDNVPIIMHDSELDTTTNVAKlFPERAREN-GKYYAVDFTL 111 Borrelia coriaceae
YP_003034128  36 KTIIAHRGASGYLPEHTLEAYSLSYGLgADYIEADVCLTKDGVPIVMHDIHLDTTTNVAKiFPDRKRKD-GRYYIIDFTL 114 Clostridium bot...
ZP_00370621   20 KLIIAHRGASAYLPEHTLESKVLAFAQgVPYIEQDVVLSKDDRLVVIHDLYLDKTSDVAQkFPERKRKD-GHYYVIDFTL 98  Campylobacter u...
O30405        25 RMIVAYRGAAGYVPEHTFASKVLAFAQgADYLQQDVVLSKDNQLIVAQSHILDNMTDVAEkFPRRQRAD-GHFYVIDFTV 103 Treponema pallidum
ZP_01042276   39 FIDIAHRGASGYLPEHSQAATVMAHALgADYIEQDVQLSRDGKAVVLHDAQLDAVTNVAEvFPERHRPD-GSYYVVDFTL 117 Idiomarina balt...
YP_003308341  19 AVVIAHRGNSGEYPENTLESFNSAKYF-ADYLEQDLQMTKDDKLVVFHDTVLDNVTNVKQvFPKERARKnGSYYVIDFTM 97  Sebaldella term...
Feature 1                                                                                        
1YDY_A       110 DEIKSLKFTEGFDiengkKVQTYPGRFPmgKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKT 189 Escherichia coli
1T8Q_A        88 DEIKSLKFTEGFDiengkKVQTYPGRFPxgKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKT 167 Escherichia coli
EAQ42617     107 DELKSLQVTERFDpk--tGEQFYPNRFPkwKANFKLHSLQEEIELIQGLNASTGNNIGIYPEIKEPKFHQKEGKNLTTTV 184 Polaribacter sp...
NP_602708    104 SELQTLEMTENFTtkdgkQTAVYPNRFPlwKSDFKLHTFEEEIEFIQGLEKSTGKKIGIYPEIKAPWFHHQNGKDIAKAT 183 Fusobacterium n...
Q06282       114 KEIQSLEMTENFEtkdgkQAQVYPNRFPlwKSHFRIHTFEDEIEFIQGLEKSTGKKVGIYPEIKAPWFHHQNGKDIATET 193 Haemophilus inf...
YP_002769765 107 DEIKKLKTTEVFTvengkQVQDYPDRFPlwKSNFSVHTLEEEIELIQGMNKSTGRNVGIYTEIKAPWFHRHEGKDISLAV 186 Brevibacillus b...
AAG24364     112 DEIKSLSISERFDpe--tREPIYPNRFPlnEYNFKIPTLEEEIQFIQGLNKSTGKNVGIYPEIKKPFWHKQQGKDISKIV 189 Borrelia coriaceae
YP_003034128 115 QEIKKLSVNERIDlk--tNEAVFKDRFPlhKSHFEVPTLEEEIQLIQGLNKSTGKNVGIYPELKNPKFHTENGQDIGSVT 192 Clostridium bot...
ZP_00370621   99 DELKSLKMSEGFKre-ndSVNVYPKRFPtkKADFTINTLEEEIELIQGLNKTLNKNVGIYVETKRPWFHKQEGKDISKLT 177 Campylobacter u...
O30405       104 EELSLLRATNSFYtrgkrHTPVYGQRFPlwKPGFRLHTFEEELQFIRGLEQTTGKKIGIYSEIKVPWFHHQEGKDIAALT 183 Treponema pallidum
ZP_01042276  118 NHLKQLSLTSRRNs---dGAARYPQRFQnnQVDFKIQTLAESLNLIQELNRVRNKNTGVYIEVKAARWYRDQDYDPLAVV 194 Idiomarina balt...
YP_003308341  98 DELKTLQVTNRYFilwkfKFEQFKNRKYstDDTAKIASFEEVLDLVEEYNKENNTRLGIYPELKDVWFYKSEGKDTTVAL 177 Sebaldella term...
Feature 1                                                                                        
1YDY_A       190 LEVLKKYGYt--gKDDKVYLQCFDADELKRIKNELepkmgmeLNLVQLIAYTDwnetqqkqpdgswvnynydwmfKPGAM 267 Escherichia coli
1T8Q_A       168 LEVLKKYGYt--gKDDKVYLQCFDADELKRIKNELepkxgxeLNLVQLIAYTDwnetqqkqpdgswvnynydwxfKPGAX 245 Escherichia coli
EAQ42617     185 LNILADYGYk--tKNDNCILQCFDAEELERIRVDLks----eLFLVQLIEHPE----------------------EAKQL 236 Polaribacter sp...
NP_602708    184 LEVLKKYGYt--kKSDMVYLQTFDYNELKRIKTELmpkmgmdLKLVQLIAYNDwheteekdkngkwvnydydwmfKEGAM 261 Fusobacterium n...
Q06282       194 LKVLKKYGYd--kKTDMVYLQTFDFNELKRIKTELlpqmgmdLKLVQLIAYTDwketqekdpkgywvnynydwmfKPGAM 271 Haemophilus inf...
YP_002769765 187 LQVLKKYGYv--sKNDKAYIQTFDPNEAKRIRTELypqlnmnVKLVQLMAETGwnetmnyengk-avpynydwmfEKGAM 263 Brevibacillus b...
AAG24364     190 IEILNQYGYk--sKEDKIYLQTFDFDELKRIREELgy----qGKLIMLVGENDwneapt----------dyeyikSQEGM 253 Borrelia coriaceae
YP_003034128 193 LKILEKYGYn--dKNSKCYLQCFDPTYLKYMKNKLkt----kCKIVQLIGLQSwednknd---------nvaqmlSKEGL 257 Clostridium bot...
ZP_00370621  178 LEVFKKYGYt--nKDSKVYFQSFDYPDLVRVKKELlpqmgmdIKLVGLIGLNEweetfefkngk-wqnydfsyllNIKNY 254 Campylobacter u...
O30405       184 LALLKKYGYq--sRSDLVYVQTYDFNELKRIKRELlpkyemnVKLIQRVAYTDqretqekdsrgkwinynynwmfEPGGM 261 Treponema pallidum
ZP_01042276  195 MNVLSKNGYsdqqQATPIYLQSFDPETLRRVKREFhc----dFPLVQLIADNAwgetpi----------dydalrTYAGL 260 Idiomarina balt...
YP_003308341 178 FDILKKYSYd--nKQDEIFIQSYDSAELQRVKNIInpeynvnYKLVQLIPKRKsgdikvfrdgk-kekydykyfyTKNGL 254 Sebaldella term...
Feature 1                                                                                        
1YDY_A       268 KQVAEYADGIGPDYHMLIeetsqp---gniklTGMVQDAQQNKLVVHPYTVRSDKLPey--tpDVNQLYDALYNk-AGVN 341 Escherichia coli
1T8Q_A       246 KQVAEYADGIGPDYHXLIeetsqp---gniklTGXVQDAQQNKLVVHPYTVRSDKLPey--tpDVNQLYDALYNk-AGVN 319 Escherichia coli
EAQ42617     237 AHFATYADGVGPWYKQILsekvn----nsfqfTNLVKEAHELGLKVHPYTFRADALAef---sSFDEMLKTLLId-ANVD 308 Polaribacter sp...
NP_602708    262 KEIAKYADGVGPGWYMLIddknsk--vgnivyTPMVKDIATTKMELHPYTVRKDALPef--ftDVNQMYDALLNk-AGAT 336 Fusobacterium n...
Q06282       272 AEVVKYADGVGPGWYMLVnkeesk--pdnivyTPLVKELAQYNVEVHPYTVRKDALPef--ftDVNQMYDALLNk-SGAT 346 Haemophilus inf...
YP_002769765 264 KEIAKYADGVGPWKPMIIkeestr---dhliiTNLVKEAHEADLDVHPYTFRADKGQipayaaSFEELLDQFYFt-AGVD 339 Brevibacillus b...
AAG24364     254 TEVAKYADGIGPWISQIIidg---------qvTDLISLAHKHNMEVHPYTFRIDALPsy--vkDANELLDLLFNk-AQVD 321 Borrelia coriaceae
YP_003034128 258 KEMAKYADGIGPWYGQILnndgkleksqdvtnPDLVADAHEAGLVVHPYTVRKDQLPky--akDADSLLRKLLFd-ANVD 334 Clostridium bot...
ZP_00370621  255 AEISKIVDGLGPTYVLLFderelk--nhkivpNNFVKNAHKYNIKVHPYTIRADALPiw--akSADELFDAILFk-AGAD 329 Campylobacter u...
O30405       262 QKIAKYADGVGPDWRMLIenewsk--vgavrlSPMVSAIQDAKLECHVHTVRKETLPsy--arTMDEMFSILFKq-TGAN 336 Treponema pallidum
ZP_01042276  261 ESLTSYVDHVGLWIGHVLkevkd----gqpvwTDVLTNAEKVGLKVHVYTLRSDQLPqg--veSLKQLRGWLKE--AGVQ 332 Idiomarina balt...
YP_003308341 255 DEIRQYADAIGPDKSLIHgnk---------skEDYYKYAKEIGFLVHAYTFNIERVGkg---fKSYQDEVKYYRdvLKVD 322 Sebaldella term...
Feature 1                
1YDY_A       342 GLFTDFPD 349 Escherichia coli
1T8Q_A       320 GLFTDFPD 327 Escherichia coli
EAQ42617     309 GAFTDFPD 316 Polaribacter sp. MED152
NP_602708    337 GVFTDFPD 344 Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Q06282       347 GVFTDFPD 354 Haemophilus influenzae
YP_002769765 340 GVFTDFPD 347 Brevibacillus brevis NBRC 100599
AAG24364     322 GIFTDFVD 329 Borrelia coriaceae
YP_003034128 335 GLFTDFTD 342 Clostridium botulinum D str. 1873
ZP_00370621  330 GVFTDFPD 337 Campylobacter upsaliensis RM3195
O30405       337 VVLTDFPD 344 Treponema pallidum
ZP_01042276  333 GVFSDFPD 340 Idiomarina baltica OS145
YP_003308341 323 GYFTDYPA 330 Sebaldella termitidis ATCC 33386

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap