Conserved Protein Domain Family
PBP2_TdcA

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cd08418: PBP2_TdcA 
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold.
TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to 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: 176110
View PSSM: cd08418
Aligned: 8 rows
Threshold Bit Score: 270.764
Threshold Setting Gi: 157963242
Created: 26-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 Burkholderia sp. DntR structure (1UTH_A)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                           #      
P0ACQ7        98 EVSFGFPSLIGFTFMSGMINKFKEVFPkAQVSMYEaqlssflPAIRDGrlDFAIGTLsaemklqdLHVEPLFESEFVLVA 177 Escherichia col...
YP_001503276  96 KVTIAVNGFIAHWLVPPLIKALTEKAPnMEIYMANwee-stsDKIINGeiQLAINYFplel-tkqLIQEKLGSDDFVVLC 173 Shewanella peal...
YP_587287     92 VVRIGATGGPAHLLLPAVLKRFRSQHPdVQVCIDSgvypahlSDLRAGvmDMAVSPIpdegiereFVSEPLYDNDSVVVA 171 Ralstonia metal...
NP_287844     96 QINIGMGASISRSLMPAVISRFHQQHPqVKVRIMEgqlvsmiNELRQGelDFTINTYyqgpydheFTFEKLLEKQFAIFC 175 Escherichia col...
YP_003002765  96 RVNIGVGASVAHTVMPEVVSRFHRLYPqVKLRITEgqlvamiHELRQGelDFTVNTYsgsaydneLLYEKLMEKEYCVVV 175 Dickeya zeae Ec...
P0ACQ9        98 EVSFGFPSLIGFTFMSGMINKFKEVFPkAQVSMYEaqlssflPAIRDGrlDFAIGTLsaemklqdLHVEPLFESEFVLVA 177 Shigella flexneri
YP_002932896  96 HVAFGISSLFGVTVLNKVLNDFKQGFPaTVINVKEaqlstllPSLRDGrlDFALGTLtdemplgdFISIPLFDAPFCIVA 175 Edwardsiella ic...
YP_001919297 101 KFSLGYSSLVGYTVLPDVINEFRELNRdVSISIYEgqlsdllPLLNTGrlDCAIGTLlndelpyeYSAELLFKSSFSVFT 180 Escherichia col...
Feature 1                                          #                                             
P0ACQ7       178 Sksrtctg----tttlesLKNEQWVLPqtn-mgYYSELLTTLqrngi-sienIVKTDSVVTIYNLVLNaDFLTVIPCDMT 251 Escherichia col...
YP_001503276 174 RkdhpfqkevigaedfpkYPLASHIVPgw--neTKNFTVEALkklgy-kprvQLSSSKMNIILSSLELtDMLLPCSKLLA 250 Shewanella peal...
YP_587287    172 Hkdhplrn----arrlreLVGSEWVLTgqrmhgPGAAILDAFraldlplprvAVRCDTIGMIQTLLEDrSLLCLLPRQLV 247 Ralstonia metal...
NP_287844    176 Rpghpaig----arsikqLLDYSWTMPtph-gsYYKQLSELLddqaq-tpqvGVVCETFSACISLVAKsDFLSILPEEMG 249 Escherichia col...
YP_003002765 176 Rrdhpiqq----arsledLLDYEWTMPtpr-gsYYKQLFDLFatlpt-tpriSVTCETLMSSVSLVAKtDFISILSRDVI 249 Dickeya zeae Ec...
P0ACQ9       178 Sksrtctg----tttlesLKNEQWVLPqtn-mgYYSELLTTLqrngi-sienIVKTDSVVTIYNLVLNaDFLTVIPCDMT 251 Shigella flexneri
YP_002932896 176 Rkdhplat----csalegLRQAKWVMPetd-mgYYHNIRHIIpfdhpdnphyPILTDSTVCIMNLVMHgDYLTILSRARL 250 Edwardsiella ic...
YP_001919297 181 Svlspysr----arnlqeLQEAKWVLPvtc-fgYYNNLTEFLrragv-nidnAIRTDSISSIINLVSCaDYVTVLAKPMG 254 Escherichia col...
Feature 1                                #                        
P0ACQ7       252 SPfg-snQFITI--PVEETLPVAQYAAVWSKnyriKKAASVLVELAKEY 297 Escherichia coli K-12
YP_001503276 251 KTlsdrfRIIDI--DPELEQPSSDFALIYANksrrNPLDEWLQQCVIDC 297 Shewanella pealeana ATCC 700345
YP_587287    248 PGqlasaNLVAL--PIEDPLPSHAVSLIYRAdspmTPVAEQFATLLRRE 294 Ralstonia metallidurans CH34
NP_287844    250 CDplhgqGLVML--PVSEILPKAAYYLIQRRdsrqTPLTASLITQFRRE 296 Escherichia coli O157:H7 EDL933
YP_003002765 250 RDpilgeRLRVL--ELEQPLPKATFYLIQRKdtmlSPMGTQLAKLFRLY 296 Dickeya zeae Ech1591
P0ACQ9       252 SPfg-snQFITI--PVEETLPVAQYAAVWSKnyriKKAASVLVELAKEY 297 Shigella flexneri
YP_002932896 251 REar-fgGVLTAlpIGLQFLPVGHYGLIYPRkrplTQASQALVEQFRWH 298 Edwardsiella ictaluri 93-146
YP_001919297 255 DGrnkklSLRPI--RIKEQLPSADYYLTWSKkyipSRLLSEFMRIIKAR 301 Escherichia coli 53638

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