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cd08488: PBP2_AmpR 
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold.
AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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.
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Statistics
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PSSM-Id: 176177
View PSSM: cd08488
Aligned: 5 rows
Threshold Bit Score: 340.278
Threshold Setting Gi: 157403315
Created: 21-Oct-2009
Updated: 17-Jan-2013
Structure
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Aligned Rows:
Hierarchy
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Display:
 
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).

cd08488 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd08488 is a member of the superfamily cl11398.
cd05466:PBP2_LTTR_substratecd08411:PBP2_OxyRcd08412:PBP2_PAO1_likecd08413:PBP2_CysB_likecd08414:PBP2_LTTR_aromatics_likecd08415:PBP2_LysR_opines_likecd08416:PBP2_MdcRcd08417:PBP2_Nitroaromatics_likecd08418:PBP2_TdcAcd08419:PBP2_CbbR_RubisCO_likecd08420:PBP2_CysL_likecd08421:PBP2_LTTR_like_1cd08422:PBP2_CrgA_likecd08423:PBP2_LTTR_like_6cd08425:PBP2_CynRcd08426:PBP2_LTTR_like_5cd08427:PBP2_LTTR_like_2cd08428:PBP2_IciA_ArgPcd08429:PBP2_NhaRcd08430:PBP2_IlvYcd08431:PBP2_HupRcd08432:PBP2_GcdR_TrpI_HvrB_AmpR_likecd08433:PBP2_Naccd08434:PBP2_GltC_likecd08435:PBP2_GbpRcd08436:PBP2_LTTR_like_3cd08437:PBP2_MleRcd08438:PBP2_CidRcd08439:PBP2_LrhA_likecd08440:PBP2_LTTR_like_4cd08441:PBP2_MetRcd08442:PBP2_YofA_SoxR_likecd08443:PBP2_CysBcd08444:PBP2_Cblcd08445:PBP2_BenM_CatM_CatRcd08446:PBP2_Chlorocatecholcd08447:PBP2_LTTR_aromatics_like_1cd08448:PBP2_LTTR_aromatics_like_2cd08449:PBP2_XapRcd08450:PBP2_HcaRcd08451:PBP2_BudRcd08452:PBP2_AlsRcd08453:PBP2_IlvRcd08456:PBP2_LysRcd08457:PBP2_OccRcd08458:PBP2_NocRcd08459:PBP2_DntR_NahR_LinR_likecd08460:PBP2_DntR_like_1cd08461:PBP2_DntR_like_3cd08462:PBP2_NodDcd08463:PBP2_DntR_like_4cd08464:PBP2_DntR_like_2cd08465:PBP2_ToxRcd08466:PBP2_LeuOcd08467:PBP2_SyrMcd08468:PBP2_Pa0477cd08469:PBP2_PnbRcd08470:PBP2_CrgA_like_1cd08471:PBP2_CrgA_like_2cd08472:PBP2_CrgA_like_3cd08473:PBP2_CrgA_like_4cd08474:PBP2_CrgA_like_5cd08475:PBP2_CrgA_like_6cd08476:PBP2_CrgA_like_7cd08477:PBP2_CrgA_like_8cd08478:PBP2_CrgAcd08479:PBP2_CrgA_like_9cd08480:PBP2_CrgA_like_10cd08481:PBP2_GcdR_likecd08482:PBP2_TrpIcd08483:PBP2_HvrBcd08484:PBP2_LTTR_beta_lactamasecd08485:PBP2_ClcRcd08486:PBP2_CbnRcd08487:PBP2_BlaAcd08488:PBP2_AmpR9909830707314092267168671589184815740331599098307073140922671686715891848157403315
cd08488 Sequence Cluster
cd08488 Sequence Cluster
Sub-family Hierarchy
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 cd08488 Branch
 Whole Hierarchy
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CD Hierarchy
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1              ## #                                                                      
gi 9909830    95 ILRVGAVGTLAVGWLLPRLRDFQNRYPfIDLRLSTnnnrVDIAAEGLDYAIRFGsgaWHGIDATRLLEAPLSPLCIPela 174
gi 15891848   95 LLFLGVVGTFAVGWLLPRLAAFQKRHPfIDVRVSTnnnrVDMAAEGLDFAIRFGqgsWHGTDAFRLFEAPLSPLCTPkla 174
gi 70731409   95 VLTVGAVGTFAVGWLLPRLEDFQARHPyVDLRLSTnnnrVDVAAEGLDYAIRFGtgaWHGIEALALLQAPLSVLCVPela 174
gi 226716867  95 PLHVGVVGTFATGWLLPRLPGFVNSHPrIDLRLSThnnrVDIAAEGLDYAVKFGsgaWQDLDATPLFEAPLSPLCTPela 174
gi 157403315  51 VVHVGAVGTFACGWLLPRLAEFARLHPsVDVRLSThnnrVDPAAEGLDYAVRFGrgtWPGMESRFLMGAPLAPLCTPaia 130
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                    ###                   #             
gi 9909830   175 relrtPVDLARHTLLRSYRADEWTQWFvaagvtgdmplprSIMFDSSLAMMEAAMQgaGIALAPplMFSRQLLSETIVQP 254
gi 15891848  175 emlkePADLMDATLLRSYRADEWSTWFaaagvspaaqvnaGIVFDTSLGMMEAALQglGVALAPpsMFSRHLTSGAVMQP 254
gi 70731409  175 rqlhsPADLLGQTLLRSYRTDEWPQWFqaaglgansllpqSVVFDSSLGMLEAALQglGVALAPplMFQRQLASGAVVQP 254
gi 226716867 175 rtlsqPADVLAHTLLRSYRADEWPQWLreagvghpvfirnSIMFDSSIGMIEAARQgaGIALAPpaMFTRALARGELVQP 254
gi 157403315 131 qqlrePAELARFALLRSYFVDDWRLWFeaaqav-pcgpinGTIFDSSLTMVQCALQnlGVALAPpsMFAREIAQGLLVQP 209
                        170       180       190
                 ....*....|....*....|....*....|.
Feature 1                                       
gi 9909830   255 FettvtMGSYWLTRLQsrtetqaMAAFRDWL 285
gi 15891848  255 FpvtisLGSYWLTRLQskpqtsaMQAFSDWL 285
gi 70731409  255 FdigivTGSYWLTRLQsraetpaMGAFKAWL 285
gi 226716867 255 FspglsTGQYWLVKLQsrqdspaMLVFSQWL 285
gi 157403315 210 FattldAGGYWLTRLAlkpagdgASAFAAWL 240

Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
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