Conserved Protein Domain Family
PBP2_HvrB

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cd08483: PBP2_HvrB 
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold.
The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.
Statistics
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PSSM-Id: 176172
View PSSM: cd08483
Aligned: 10 rows
Threshold Bit Score: 287.319
Threshold Setting Gi: 1170431
Created: 19-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Vibrio Parahaemolyticus GcdR-like structure (2QSX_A).

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             ## #                                                                      
P42507       99 ALTVTVPPvFASEWLMPRLARFWKKHPdIPLSLLPdarlVDLKEIgaNIGIRFGvgkWPGVISVFLTAAPQVVVAAPell 178 Rhodobacter caps...
AAA53542     99 ALTVTVPPvFASEWLMPRLARFWKKHPdIPLSLLPdarlVDLKEIgaNIGIRFGvgkWPGVISVFLTAAPQVVVAAPell 178 Rhodobacter caps...
ZP_01013679  96 PITVTLTPsFAEAWLMPRMGQFWSQHPeVEVRLVPsmalANLRRDgiDLAIRFGngdWPGNDVEPLAVSQFVVVAAPtyt 175 Rhodobacterales ...
ZP_01154996  96 ALRVALTPsFAANWLMPKISGFWLKHPeVTLELMPnndlVDLRADgiDLAIRYGrggWPGLDSEPLVVASLYAVGAPgry 175 Oceanicola granu...
ZP_05064616  96 PIRVALTPsLATNWLMPRIGAFWDMYPdIELELLPagklVDLRRDnvDVALRYGkggWTGAKVTKLMAAGHVAVAAPnyl 175 Octadecabacter a...
ZP_05741950  96 PLHVTCTPmFATHWLMPRLAGFRQAYPeVDLVIDPtgevVQLTPGgiDVALRYGsgdWPGLEAEMLLASPMVVVAAPgll 175 Silicibacter sp....
ZP_05114303  91 PLNITMTPsFAVSWLMPRINDFRHKHPdIELMLNPsadvTELAPGgtDLAIRFGrgnWPGLEAELFLATNFVVVGANcli 170 Labrenzia alexan...
ZP_01444013  96 PLEISATPgFAAVWLMPRLPLFRTRHPeISLTIDPsaalRTLEPGglDVAIRYGngdWPGLESTLLVLSPIVVVAATdlv 175 Roseovarius sp. ...
ZP_05343294  96 PLTLSVTPtFAENWLMPRLGSFWAAHPkIALSIIPsrtvVDLRSDrvDVALRYGdgdWSGVHVSPLTTPSFVVVGRPslf 175 Thalassiobium sp...
ZP_01746091  96 PLLISTTPtFASGWLLPRLASFRAEHPeINLMIDPsadvRGLEPGgiDMALRYGngsWPGLQSELFVRSPIVVVAAPglv 175 Sagittula stella...
Feature 1                                                   ###                   #             
P42507      179 ggrkklslremamlPWVREgdwpeqmqllesmglvpaALKFVDFPNEELALAAAREGIGLHLETeaLIVEDLKLGWLVKI 258 Rhodobacter caps...
AAA53542    179 ggrkklslremamlPWVREgdwpeqmqllesmglvpaALKFVDFPNEELALAAAREGIGLHLETeaLIVEDLKLGWLVKI 258 Rhodobacter caps...
ZP_01013679 176 kartldelgglsahDWFFSaaaneqrvwgkaigvdfdKVGAQDMANNGMVLSAARAGLGLSIQSkaLVAPDLDSGQLTTL 255 Rhodobacterales ...
ZP_01154996 176 rategeglaqfageTWILDrgareeqiwalshgidlaEERVLQFDSAQLAMEAAKAGLGITILPrpILLADIRAGRLTVL 255 Oceanicola granu...
ZP_05064616 176 kdrtvdclsdlkgtRWLMGrsqteerfwlaannidleLENVTVFQTDQLSREAARAGLGISVIPapIAEPHIAAGTFIAL 255 Octadecabacter a...
ZP_05741950 176 dqravkqpedlldlPWLEEigtneasvwlrsrgvedsLKAGRVVLPGNLLMEALRAGQGVAVSVreFVAPDVAAGRLTEL 255 Silicibacter sp....
ZP_05114303 171 gdrkmdkpedilefPWLQEygtnelalwlekqgvvpkNKLSVTHLPGYMVLEGLRRGEGISATAktFIQPDIDAGNLKVL 250 Labrenzia alexan...
ZP_01444013 176 geceiaspadlrpfPWLQElgtneatdwfaehgveqdRSRGMTGLPGNMMIEAARQGQGVAITArlFVEPDIQAGRLRLL 255 Roseovarius sp. ...
ZP_05343294 176 dgslraseakqrrkPWFFEagrseywywardmglvgdDTPYTRLETNQLVISAVRSGYGLCVQAraLVEQDVESGRLAIY 255 Thalassiobium sp...
ZP_01746091 176 gdrpiespadlshlHWLQEygtneatswfaqfgierdSGLGFTSLPGNMMLEAARQGQGVAILArvFAEPDIAAGRLRLL 255 Sagittula stella...
Feature 1                                      
P42507      259 hel-teESLGYYIVRPpgrlnpaAKIFIDWL 288 Rhodobacter capsulatus
AAA53542    259 hel-teESLGYYIVRPpgrlnpaAKIFIDWL 288 Rhodobacter capsulatus
ZP_01013679 256 yeg-dpEGLGYYIVTRpgvlspgARAFRAWL 285 Rhodobacterales bacterium HTCC2654
ZP_01154996 256 gaq-eeAEVAYHLLTRpgtisqaRDLFVRWL 285 Oceanicola granulosus HTCC2516
ZP_05064616 256 cye-enSAAAYHILTRpevvspqRDVFVRWL 285 Octadecabacter antarcticus 238
ZP_05741950 256 fc--eeQGRGYHIVHRpgvlrpgARHFVNWL 284 Silicibacter sp. TrichCH4B
ZP_05114303 251 feegvyPGTGYHLVTRpgvkrpaLKSFISWL 281 Labrenzia alexandrii DFL-11
ZP_01444013 256 fe--dtRKKGYYLVTRpgvarppLRHFVSWL 284 Roseovarius sp. HTCC2601
ZP_05343294 256 ced-reTALRYHVVTMqpp-egrIKTFVDWV 284 Thalassiobium sp. R2A62
ZP_01746091 256 fe--dtRSKGYWIVTRpgvprppLKAFLRWL 284 Sagittula stellata E-37

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