2WOK


Conserved Protein Domain Family
PBP2_clavulanate_OppA2

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cd08506: PBP2_clavulanate_OppA2 
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The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold.
Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains 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. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 173871
View PSSM: cd08506
Aligned: 31 rows
Threshold Bit Score: 359.266
Threshold Setting Gi: 21637130
Created: 27-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide binding
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Structure:2WOK_A; Oligopeptide-binding protein 2 (OppA2) from Streptomyces clavuligerus binds the Bradykinin peptide, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                          # #  #                                                        
2WOK_A        34 TLRLVSsadvdsLDPARTYyVWVWLLQrllNRTLMAYPtdpg---pagLVPAPDLAEGPGEvsd-----ggrTWTYRLRR 105 Streptomyces cl...
YP_192121     44 TLHLTAdgpggtLDPQINYgTQYMQVFvnmYDPLLTFRlarg---tagLEVVPDLADAMPQisp-----dglTWRLHLRP 115 Gluconobacter o...
YP_001506410  65 TLRLLTgrm-ptGDPGWADeLGERAFArlvTRQLYSYPadad--tarsTIPRPDLAAGAPVvtm-----ggtVYTVRLRS 136 Frankia sp. EAN...
AAM70346      18 TLRLLGpaavhqADPAAAWsPAERQLLrlcTRQLISYRpepdpgdwraLAPVADLATDVPStynaglgashrSYVVHLRP 97  Micromonospora ...
AAM70342      13 TLRYYGpggldhLDPAAAYyAFSHQVIrlfARQLFSYPtted---aaaLVPVPDVAAELPTvdngglsedgrTYTIRLRD 89  Micromonospora ...
YP_888816     42 TLRIASvedidaLDPLIAYsAESWQVIratTRQLVTYPgskeg-igddTTVVPDLAESWDVspd------rkTYTFHLRD 114 Mycobacterium s...
YP_002547441  49 TMTLAAvsaagtIDPAINYtGQYWQVLqmtNDGLVKFKqaag---tegFKIVPDVAEAIPEpqd-----dgkTYVFKIRK 120 Agrobacterium v...
YP_427265     42 SLRLLAragggtLDPHINYtAQYFQTNfilYDGLVGFKkang---kdgNAIVADLAEALPTvsd-----dgkTYTFTLRK 113 Rhodospirillum ...
YP_002277194  41 TLRLTAassggtVDPQINYtSKYAQLFavlYDGLLASRkadd---dssDDVVPDLAESVPVaed-----ggrTWRMVLRR 112 Gluconacetobact...
NP_102371     34 TIRLLArsaagtLDPHINYtDQGWQMYqpiYDGLVAFRkaeg---mdgFTIVPDLAEALPQvsn-----dgkTFTFKLRK 105 Mesorhizobium l...
Feature 1                                                                                        
2WOK_A       106 gLRYDDGTP--ITSDDVRHAVQRVFAqdvlpggptyliplldd----------------perpypgpyrtdeplrsVLTP 167 Streptomyces cl...
YP_192121    116 gLHFSDGAP--VRVEDVVASFRRIYRagsptaasfyggiag--------------------aaecletpdrcmlpgVEGH 173 Gluconobacter o...
YP_001506410 137 aARWNTPNQrrITATDVARGLKRMCAppspsplrgyyaatvvgfaeyc------aelaaapvadapaliesgtvpgIEVI 210 Frankia sp. EAN...
AAM70346      98 gVLWDTPTPrpVTAHDVVRGFKRLANpltrhpalayfrgtlrgmgrycdeyaaavaghpvtaallagfqdaheipgVFAV 177 Micromonospora ...
AAM70342      90 gVRWDTAPPrpVTAGDFVRGFKRMANpvagagaiayytstiagmaefaegyrarfagrtptaaeladyqngheisgLWAK 169 Micromonospora ...
YP_888816    115 nITFSGASNreITAHDFVYAVKRFPDpnaqvsaityfnatfdgfeeyaae---fakvptgdlaavkqfidtheirgFKAL 191 Mycobacterium s...
YP_002547441 121 gIMFSTGQE--LKPSDVAASFQRIFKvngpttgsfyngivga-------------------dkciadaanctleggVIAD 179 Agrobacterium v...
YP_427265    114 gVRFSNGQP--VTTGDVVASFQRIFKvssptagtfyngilga-------------------dhclaepagctlaegVSAD 172 Rhodospirillum ...
YP_002277194 113 gVRFSTGRE--VTVADVAASFRRLFQvgsptagsfygaiiga-------------------daclrdparctlqggLEVD 171 Gluconacetobact...
NP_102371    106 gIKFSSGQD--MGVKDVVASFQRIFKvsgptsgtfyagivga-------------------dkcladtknctleggVVGD 164 Mesorhizobium l...
Feature 1                                                                                        
2WOK_A       168 D-EHTIVFRLtrpfsDFDHLmaqPCAAPVPrrsdtg-----adygrdPRSSGPYRVARHEPdTLLHLERNPHWDrat-dp 240 Streptomyces cl...
YP_192121    174 PeTGEIVFHLtkpdgEFLYKlafPHAVILPastpvh-----dmggatVPGTGPYRITQYDPgHGMVLERNPYFHvwnpqa 248 Gluconobacter o...
YP_001506410 211 G-DDTLAFHLikpvnDFVDIlalPASSPVPlealaypp-dsqqyldnLISDGPYRFVSEPG-GGYRLSRNPAWSgss-dg 286 Frankia sp. EAN...
AAM70346     178 D-DETVVFELdrpalDFVDMlaqSGASPAPveydahlp-gsaglhehLVANGPYRVVSWRPgGTIRLEPNPAWRaet-dp 254 Micromonospora ...
AAM70342     170 D-DRTLVIELlrpanDMLNLlamPFASAAPrefddlvp-dgpdfarlVRSNGPYRITGYARgSHLTMDHNPAWRada-dp 246 Micromonospora ...
YP_888816    192 D-DKTLQLTLtepasDILDIltlNFVTPLPeevtskyfadslefrknYVSSGPYHIESYDQgKQLTLARVPEYNseg--d 268 Mycobacterium s...
YP_002547441 180 DaAGTVTIHLtqadsEFFDKmavPHASILPadtpak-----dagttaLPATGPYMIASYNPnEKMVLKRNPHFKewsvda 254 Agrobacterium v...
YP_427265    173 PaSGTIVIKLaaadaEFLQKlslPHAAILPadapak-----dvgtdaIPGTGPYKIESYDPnTRLRLVRNPYFKewskda 247 Rhodospirillum ...
YP_002277194 172 AaTRAVTFHLsrpdaEFPQKltfPHAAILPadtpvr-----dlgnvpAPTTGPYMFASYDPdRGMLLVRNPYFHvwspga 246 Gluconacetobact...
NP_102371    165 EaAGTITLNLtkpdaEILYKlalPHAVVLPadtpae-----dmgskpIPSTGAYMISAFDPnKGMTVSRNPNFKqwseea 239 Mesorhizobium l...
Feature 1                                                                                        
2WOK_A       241 iRPALPDRVELTIgldvd-vldaRLIAGefDINLegrglqhaaqrratadevlrsHTDNPRTs--fLHFVAMQphip--- 314 Streptomyces cl...
YP_192121    249 qTDGFVDRIEYDFglsde-aqvtAVEQGryDWMLdakpadrlg----elgahytsQVHIEPLl--gLYYLAMNthek--- 318 Gluconobacter o...
YP_001506410 287 iRRALPDHITVTDgldpa-titaRIEAGdaDMALsgdipaddl---arlvesadkKLVVAPTgpvvALVVGLNgpsa--- 359 Frankia sp. EAN...
AAM70346     255 iRERRFDAVEFRVamggpreladRLAADdaDLPWg-------------------vPIGPVPGqr-lDPCLVFNlrdpa-- 312 Micromonospora ...
AAM70342     247 iRRRYVDRIEVRMarvsdervraEIESGaaDLSWgaavgr----------prrrtAADRNLGwa-lNPYLAFNlhsphe- 314 Micromonospora ...
YP_888816    269 pRKAYADKIVFDTtvasadaasqQLQTGtaDIALyvrsfpanvi--aqykrtdpdHLHSSASg--sAVFISWNnpaepat 344 Mycobacterium s...
YP_002547441 255 qPDGYADEIVYQFgmtee-atinAIQNGqvDWMFdtppadrlp----elgskyakQMHIDPLa--aFWYLPMNtnla--- 324 Agrobacterium v...
YP_427265    248 qPDGYVDEINYDFgltee-aaitAIQNGqaDWMFdppppdrlp----elgtkyakQVHLNLLa--aMWYAPMNvnla--- 317 Rhodospirillum ...
YP_002277194 247 qPDGYADRIQYDFglpde-aevtAVENGqyDWMFdmkpldrlg----elggrhtaQVHIRPLy--gLYYVPMNvnip--- 316 Gluconacetobact...
NP_102371    240 qPDGYPDVVQYDFglsee-aavtAIQNGeaDWMFdalpsdrlg----elgsksmdQLHISPLs--aWWYAPLNnrla--- 309 Mesorhizobium l...
Feature 1                                                                                        
2WOK_A       315 ----pfdNVHVRRAVQYAADKILLQDARGgpvNGGDLt---TALFPPTLPAHQDldlyp--------tgpdlRGDLDAAR 379 Streptomyces cl...
YP_192121    319 ----pftDVRVRRAVSMAVNRHAMTILFGg-sAISEPl---CQMVPHGIPGADLgl--------------dcPQDLEGAR 376 Gluconobacter o...
YP_001506410 360 ---aalrDQQAREALAYCIDRTAVAAALGg-pMLATAt---AQLLQSPMTGYETynpfp---------agdgSGDSRRCA 423 Frankia sp. EAN...
AAM70346     313 --npavaDAAVRRVVAGAVDRAALVRIARaadPWSEVra-aHTVVPPGNDGHRQpdpl----------tdpiPDADADPR 379 Micromonospora ...
AAM70342     315 --rgalrDRTVRLAIAYAVDKARLVRFFDd-mNIGTVtrpaHTAIPPGNFGHREydpyp---------tpgdRGDRARCR 382 Micromonospora ...
YP_888816    345 paqaalkDLKVRQAVNYSLNRADVVRGLGg-pDSAIPs---NEILTSTTLGFNDenpyp---------tpedKGDPDKAK 411 Mycobacterium s...
YP_002547441 325 ----pfnNIKVRQAVNYALDRDALVGLFGg-dALASPt---CQILPPDFPGYAPnclytkn-----pgeswsEPDMDKAK 391 Agrobacterium v...
YP_427265    318 ----pfnDERVRKAVNYAVDRGALTKLFGg-aNLATPa---CQILPPDFPSYEAycpytqa-----pgakwsKPDLEKAK 384 Rhodospirillum ...
YP_002277194 317 ----pfdNPLARQAVNFAMDRRAMAILYGg-tAVATPl---CRMVPPGLPGALAdcaytaggnsdhplpswrAPDLDRAR 388 Gluconacetobact...
NP_102371    310 ----pfdNEKARQAVAYAIDRNTLVKLFGg-kVLASPv---CQVLPPDFPGHEDycpftkn-----pgakwsAPDLDKAK 376 Mesorhizobium l...
Feature 1                          #                                     #                    ## 
2WOK_A       380 AELAAAGLpdGFRAVIGTQRGk-fRLVADAVVESLARVGIELTVKel----dVATYFSLGAGhpetvrehglgLLVTDWg 454 Streptomyces cl...
YP_192121    377 RLIHEAGAd-GASVTLVVPNRameLGMGTYLRNALQSAGLNVQLRpit-aglAESYEQNSANhv--------qIALSYWf 446 Gluconobacter o...
YP_001506410 424 DGLANNPGgkVTALSLLTTDSatdTAVAEALRAAFARAGIRLDLRir----tGAQYTAAASSpggqfwdlaltTITPDWf 499 Frankia sp. EAN...
AAM70346     380 ERLAAAGHpdGLTLTAVHPDTaedLALARSWAADLGAAGIDVRLValddanhRALLAATGDApglrw-dlataTFTAPWa 458 Micromonospora ...
AAM70342     383 ELLAEAGYpdGLRLTMIYRIDavhGQVAKAIAEDLGAGGVDVRLVei---dqTDEYYRILQDparaa-agewdITPAAWm 458 Micromonospora ...
YP_888816    412 ALLADSGHk-DLTLSAAYRNTpefEKIATSVQNALARSGITLRLVpia--gdSWGAFRAYLAdksnl--dqwdLAITTWt 486 Mycobacterium s...
YP_002547441 392 ALIKESGTa-GQKVTIIAEDNavgRGIGTYVQSLLNELGYDASLKais-pniEFTYIQNTNNnv--------qISVTQWy 461 Agrobacterium v...
YP_427265    385 ALVKDSGTa-GQKVTVIVEDNavaRSIGVYLQGVLAQLGYDASVKpis-qniQFTYIQNTANav--------qISVSQWy 454 Rhodospirillum ...
YP_002277194 389 RLVAQSGTa-GQKVTVVVLNTavdLSMGVWLRNMLQSLGYDASVKpma-esvQFGYVQNTANhv--------qISVRDWf 458 Gluconacetobact...
NP_102371    377 QLVEESGTk-GQKVTIIAEDTaisRSIGVYLQSVLTSIGYVADVKpis-pniQFTYIQNTNNkv--------qMSITQWy 446 Mesorhizobium l...
Feature 1                                                                                        
2WOK_A       455 adfp--teygFLAPLVDGRqikrngg-nwnlpeLDDPEVNALIDETlh--ttDPAARAELWRAVERRVMEhAVLLPLVHD 529 Streptomyces cl...
YP_192121    447 adyp--sastFLDDLFGCDnyhpnsavspnftgFCDQHVQTLFDQArs--qtDPTKAAPIWQEAGHAIMEqMPGAPMIQM 522 Gluconobacter o...
YP_001506410 500 gda----grtVYEPLLDEAwvgar----padggYRRPDLLARYESAvt--asSEDDAATDWAGLERTVLNdAAIVPLAVT 569 Frankia sp. EAN...
AAM70346     459 ygn----arvFLQPLVGEGpgn--------pggYRDPGVDRVVERAld--aaDPREAVALWQEVERRLLAdAAVVPLLFR 524 Micromonospora ...
AAM70342     459 pdwfgnngrsYVQPMFQSNtgvgt----anyggYHNPLVDELIDRAls--arTEAEAEELWHRVDRQVLQdVAIVPILAC 532 Micromonospora ...
YP_888816    487 pdwqgnsarmTLGGWLNSDfapggt---wngvtYHNPQLNAAAARAf-----AAADPTADWKEANRIASAdLAWFPLIER 558 Mycobacterium s...
YP_002547441 462 mdyp--aasdFINVLLSCDsihpgsdssiniagYCNKELDKQMQDTmslsikNPKAADANWAKIDKAFMEqAPLAPLFTP 539 Agrobacterium v...
YP_427265    455 qdyp--aasnFLNVLFSCGsfhpgsdssinmsgFCDKTIDAQITEAlvtatkDPAKAATQWTAIDKAITDkAPVAVLFTP 532 Rhodospirillum ...
YP_002277194 459 adyp--sasnFLDDLFGCEnfhpgtdnsinisgYCNAAAQAAMDAAkq--etDPARAAMLWTEAERTIDRdSPAVPTVRI 534 Gluconacetobact...
NP_102371    447 kdyp--aasdFLNILFSCSsfregsdasiniagFCDKDIDAKMQKAldlgvtDQKAADKMWAEIDKQVTDkAPAVGLFTP 524 Mesorhizobium l...
Feature 1                         
2WOK_A       530 k--tLHFRNP--WVTNV 542 Streptomyces clavuligerus
YP_192121    523 r--tVDFVSK--RLGNY 535 Gluconobacter oxydans 621H
YP_001506410 570 h--tLRLRSS--AVQAF 582 Frankia sp. EAN1pec
AAM70346     525 r--aTDAAPRgpRVRRA 539 Micromonospora echinospora
AAM70342     533 eptiEHLTSS--RVRGA 547 Micromonospora echinospora
YP_888816    559 v--kTIPTSD--RVTNW 571 Mycobacterium smegmatis str. MC2 155
YP_002547441 540 k--sVNFTSA--RLGNY 552 Agrobacterium vitis S4
YP_427265    533 k--qVTFLSA--RVKGF 545 Rhodospirillum rubrum ATCC 11170
YP_002277194 535 n--yIDFVSR--RLGHY 547 Gluconacetobacter diazotrophicus PAl 5
NP_102371    525 k--rLDFVSK--RVGNF 537 Mesorhizobium loti MAFF303099

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