1UQW,2D5W,2O7I,1JET,1XOC,1DPP,2WOK,1ZLQ,3DRF,2GRV


Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like

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cd00995: PBP2_NikA_DppA_OppA_like 
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The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold.
This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel. 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 of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 173853
View PSSM: cd00995
Aligned: 354 rows
Threshold Bit Score: 152.077
Threshold Setting Gi: 112490880
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
1UQW_A        26 DVVVAVgsn----fttLDPYDand------tlSQAVAks----fYQGLFGLDke-------xKLKNV---LAESYTVsdd 81  Escherichia coli
ZP_03761138   77 VLRVYTnda-----tgVINPAyas-----sagDRAVSav----iFEPLMRKSvd-------gKLEPV---LARQVRMaed 132 Clostridium asp...
ZP_01216339   32 NVIIAVtql----penFSPYAns-------plSLSYAhl----fFDPLVRWGin-------gKLEKR---LLRDWRVik- 85  Psychromonas sp...
ZP_02025864   57 TVDKVTigln--dnwnDISPFgtm-----samRTAIMyn----fYEYAAVRKd--------fGCSLEd--MELECAKei- 114 Eubacterium ven...
A1JJG7       120 HILRVLyyrp---lqnLLPGTalr------rsETHMVrq----iFNGLTRINee------ngELEPD---LSHHWQAis- 176 Yersinia entero...
ZP_02211897   44 NLTMIKpt-------tINPILnnd------ksVSYVLnl----vYDSLFEFDen-------yNLQPK---LVDSYNIssn 96  Clostridium bar...
EEO35103      33 KIRISQelr----vttLDPIKltd------iySKRAFrf----iYDTLFEIDid-------gKITPK---LAQEYYYit- 87  Fusobacterium m...
AAN63879      81 DFNEPIwd-------aGDKGTie-------taNAFAFed----dGDDFFHANvd-------gYFVYYy--PSEAGTFg-- 131 Chinook salmon
YP_001621198  91 RVPRMAagepvdvngdGTVWEitlrtdlkfqdGTPINantfdysWRQLLDPDqlnvrasnlyDASNLplvNAEAYTKqks 170 Acholeplasma la...
ZP_03293998   42 EIQLAIqkp-----ntINPVTntd------esVLNVLnl----vYDGLFELNkn-------yNAIPK---LVKNSNMspd 96  Clostridium hir...
1UQW_A        82 ---------------------------------------------------------giTYTVKLREg-----------I 93  Escherichia coli
ZP_03761138  133 ---------------------------------------------------------gaTCTIQLKKn-----------I 144 Clostridium asp...
ZP_01216339   86 ---------------------------------------------------------pgVIRFYLKNn-----------I 97  Psychromonas sp...
ZP_02025864  115 ---------------------------------------------------------nkVDDLTYDV------------V 125 Eubacterium ven...
A1JJG7       177 ---------------------------------------------------------plHWRFYLRPa-----------I 188 Yersinia entero...
ZP_02211897   97 ---------------------------------------------------------nkSIDITLKEn-----------I 108 Clostridium bar...
EEO35103      88 ---------------------------------------------------------kkLLYIKLKDg-----------I 99  Fusobacterium m...
AAN63879     132 ----------------------------------------------------------gNWDLLYGKdggg-----yggW 148 Chinook salmon
YP_001621198 171 pksdsfgefvwlvdgkevsianayshevggydyyfatvegyfvefygasyasyfprnysNWALTLEDgsllaedaagnlS 250 Acholeplasma la...
ZP_03293998   97 ---------------------------------------------------------gkQMDIVLKD------------A 107 Clostridium hir...
1UQW_A        94 KFQD--GTD---------FNAAAVKANLDRASDpanhlkrh-------------------nlykniakTEAIDPTTVKIT 143 Escherichia coli
ZP_03761138  145 RFSD--GQA---------LTARDAAFSIAAMCVtaeegsgpygniqg-------vrafregagelpegIRVTDELTVELA 206 Clostridium asp...
ZP_01216339   98 YFHS--GNR---------LTSNDVLWSYAQIKKrakfkff----------------------fsaikkISRVNTHTFDID 144 Psychromonas sp...
ZP_02025864  126 FYDN--IKD---------AAGNEITAEIKLSDN-----------------------------------PLGTIEYILNIV 159 Eubacterium ven...
A1JJG7       189 HFHH--GRE---------LEMNDVITSLTRLIPqplfs--------------------------hitaVRSPTPYVIDVH 231 Yersinia entero...
ZP_02211897  109 KWHN--GQS---------LTASDVKYTYDLIKKntdssyys--------------------lvsniskISVNGSKNLTIT 157 Clostridium bar...
EEO35103     100 KFQD--GTS---------LTSEDVKNSLLRVKTqgalkef----------------------yknieeIEIINNREFIIK 146 Fusobacterium m...
AAN63879     149 VLQDadGVPtvlpdgtpnPAAGEKAKYYQGAKPklfyedgtvvpvgekgqpvgataipndpvswdkvgFKVTGTHKFQIT 228 Chinook salmon
YP_001621198 251 KLPN--GDAnp------aFDAESAQEGYVSGRPqlrfedgavvpvaengdpvggtkipndpvawanvgFKVTGTHKFQIT 322 Acholeplasma la...
ZP_03293998  108 KWHD--GNP---------ITADDVAFTVSSIRSnktspyny--------------------mvqnisdVTVNGEKELTIK 156 Clostridium hir...
1UQW_A       144 lkq--pfsAFINIlahpataxispa----------alekygkeigfyPVGTGPYELDTWNQtDFVKVKKFAGYWqp---- 207 Escherichia coli
ZP_03761138  207 fet--pspDNLRIletkiqerpenlt--------sgflpvlqqlsmdGTGTGAYQKVRIRDgSGIRLETNEFYRg----- 271 Clostridium asp...
ZP_01216339  145 stl--sqdELLDYlsdffvldeqyythlnvenspfppitrstalmpmVSGTGPYKLRAFNInLALQVTADKNYWd----- 217 Psychromonas sp...
ZP_02025864  160 --------PVISKkayedsg---------------------dgmttkPVTTAAYQVKEMIAgSTITLEKNKDYWqtddsk 210 Eubacterium ven...
A1JJG7       232 lsa--pdnWLPWLlgsvhamilpq------------ewenqpdfrrhPIGTGPYSVIRNHQ-SQLKIQAFDNYFg----- 291 Yersinia entero...
ZP_02211897  158 fkd--gyaFSLETlifpivskdkldn---------lksdklklasnnLIGNGAYKIKTYEDrNYMLLELNKDYYdl---- 222 Clostridium bar...
EEO35103     147 fsq--edkYIFETlshtmssi-------------------ikekagkIIGTGLYQVEALQK-DSVTLSNIEFPYk----- 199 Fusobacterium m...
AAN63879     229 ltepkdawYVKGQlmsgitgvvheakyeag-ksadkrtttygtidnpLVSYGAYNLIEWQDgVLYLFERNDKHYaa---- 303 Chinook salmon
YP_001621198 323 ltepkdawYVKGQlmsgitgvvheakyeag-ksadkrtttygtidnpLVSYGAYNLIEWQDgVLYLYERNDDHYaa---- 397 Acholeplasma la...
ZP_03293998  157 fkn--naaFAKENltfpiiskvql------------sgkdinnvdanKVGNGVYKIASYSDrEGISLEVNKDYYgd---- 218 Clostridium hir...
1UQW_A       208 ----gLPKLDSITWRPvadnntraaXLQTGeaQFAFpipyeqat----lleknkniELXASPSixQRYISXNvtqk---- 275 Escherichia coli
ZP_03761138  272 ----kIRDIKAVEFVTygty-emgtVIDEQriDAAFfsaesalfd---rffsakqfTIYEKPGagLFYMALNrnnr---- 339 Clostridium asp...
ZP_01216339  218 ----aQENTLDITFLKiksqrarvyALLSGdvDISHavlkkqiq----sieveknkQLVSIGSsrSFYLSLSgkhs---- 285 Psychromonas sp...
ZP_02025864  211 rssvsTTNVDTIVYKVvteasqmatAIQTGdiDVAQymdttaidpfyangkatngyQVEQLNSnmMFTVLPNmskds--- 287 Eubacterium ven...
A1JJG7       292 ----fRALIDEVNIWVlpe---lseELVYSgvQLQAddt--------------sknELESRLEegCYFLLFDqrsp---- 346 Yersinia entero...
ZP_02211897  223 ---dkNNNKKEVYVKMvpdnesqteMVLSLdsDVSRvtlgsisk-----fvdndnfVINKYQGrnYDYVLFNydne---- 290 Clostridium bar...
EEO35103     200 -----KIIIDRIFSIQdrll-slfnNNSDViyDITNfdikngknl---kiidekniDIKKSENivTTALVFNkn------ 264 Fusobacterium m...
AAN63879     304 ----eEYRIKRIRYDViadqsiavnEFKAGrlDIVGasgeyfk-------efkespQLKLTPStvFFRFAFNiderpdgt 372 Chinook salmon
YP_001621198 398 ----eEYRIKRIRYDViadqsiavnEFKAGrlDIVGasgeyfk-------efkdspTLKLTPAttFFRFAFNiderpdgt 466 Acholeplasma la...
ZP_03293998  219 ---vpKSAMNINVNIVpned-avvsTVEALesDMVKadsdnls------rfqnnrfDIMSYEGrdYDAVLINqtnp---- 284 Clostridium hir...
1UQW_A       276 ---pfdNPKVREALNYAINR-PALVKVAFa--------GYATPatgvvppsia-------------------yaqsykpw 324 Escherichia coli
ZP_03761138  340 ---qlyIPAVRRAIALSIDR-DRFAGGNLs--------AYMVKaeaigpeds--------------------iyaggenm 387 Clostridium asp...
ZP_01216339  286 --sllkVASARKAISLAINQ-QGMLDNILq--------GLGHInstyspllt--------------------resiglnn 334 Psychromonas sp...
ZP_02025864  288 --ilstSKELREAIYYAINA-EDCLKASCg--------GYGETlsamanplsgdy---------------veswkdrdyy 341 Eubacterium ven...
A1JJG7       347 ---ltrNPDIRRWLCELITP-VALLSHADpfyqrywspAYGMLpr----------------------------------- 387 Yersinia entero...
ZP_02211897  291 ---ylkNLDIRKAISFAVDR-NSIIKDAYs--------NRAKLtnfplnstsv------------------yydnelkpl 340 Clostridium bar...
EEO35103     265 -----rDLKFKKILNNILNTeESLLPPEIy--------DKNLEdidk-------------------------------vk 300 Fusobacterium m...
AAN63879     373 tnpilgYKEFRQAFYYAIDR-EEFASEVR---------APAYAnqgfigpvyiateygsvsyrgsdagkavfaplspett 442 Chinook salmon
YP_001621198 467 tnpiltYKEFRQAFYYAIDR-EEFASEVR---------APAYAnqgfigpvyiateygsvsyrgsdagkavfaplspett 536 Acholeplasma la...
ZP_03293998  285 ---llaNANFRKAIVSAINR-ETIIENGYm--------GNIHSvnipinsksr------------------yyessiknm 334 Clostridium hir...
1UQW_A       325 pYDPVKARELLKEAGYpn-------------------------------------------------------------- 342 Escherichia coli
ZP_03761138  388 aLNREKAKKLMEEAGEkygs------------------------------------------------------------ 407 Clostridium asp...
ZP_01216339  335 eYNVKKARELLTKMEIss-------------------------------------------------------------- 352 Psychromonas sp...
ZP_02025864  342 nYNIETAKQKLKDSGVdvs------------------------------------------------------------- 360 Eubacterium ven...
A1JJG7       388 wHHNRLRVLETKPEGLt--------------------------------------------------------------- 404 Yersinia entero...
ZP_02211897  341 sYNTENANNYLKKAVLslsktddnkekdttddkdntde------------------------------------------ 378 Clostridium bar...
EEO35103     301 nFNINKELNTLNDKEKivelmi---------------------------------------------------------- 322 Fusobacterium m...
AAN63879     443 gFNPTKAKQLFDAAYAkavadnk--------------------------------------------------------- 465 Chinook salmon
YP_001621198 537 gFNPTKAKQLFDAAYAksvadgn--------------------------------------------------------- 559 Acholeplasma la...
ZP_03293998  335 eYSTENAAKYMKDIKInkkdkiqetqvnatnkpnnkvngsggsnkvnpskkpsnsgntggtsnntggssnsgadanqgsg 414 Clostridium hir...
1UQW_A       343 -----------------------------------------------------gfSTTLWSShnh--------------- 354 Escherichia coli
ZP_03761138  408 ----------------------------------------------------lkgRLRLPVLagn--------------- 420 Clostridium asp...
ZP_01216339  353 ------------------------------------------------------qQLTLLTFksnr-------------- 364 Psychromonas sp...
ZP_02025864  361 -----------------------------------------------------gkTLKILTQpaf--------------- 372 Eubacterium ven...
A1JJG7       405 -------------------------------------------------------ELTLTFYshh--------------- 414 Yersinia entero...
ZP_02211897  379 ---------------------------------ekteaddkatnnkentsdkkddKKDLKDSkkgr-------------- 411 Clostridium bar...
EEO35103     323 --------------------------------------------------lnteeDRKLAENikn--------------- 337 Fusobacterium m...
AAN63879     466 ------------------------------------------------isdgqkvSVEYTYYkve--------------- 482 Chinook salmon
YP_001621198 560 ------------------------------------------------iadgdkvTVEYTYYkve--------------- 576 Acholeplasma la...
ZP_03293998  415 eqagggasggqsnggssggasggesagsggesggearnietreetrdivyateedKEEFEKIanensdsviatnlvrttn 494 Clostridium hir...
1UQW_A       355 -------------------------------------------------------------------------staQKVL 361 Escherichia coli
ZP_03761138  421 -------------------------------------------------------------------------knqETLA 427 Clostridium asp...
ZP_01216339  365 -------------------------------------------------------------------------vdhEEVL 371 Psychromonas sp...
ZP_02025864  373 --------------------------------------------------------------------------nlDKVA 378 Eubacterium ven...
A1JJG7       415 -------------------------------------------------------------------------sefDAIS 421 Yersinia entero...
ZP_02211897  412 -------------------------------------------------------------------------yfkDVTN 418 Clostridium bar...
EEO35103     338 --------------------------------------------------------------------------rlKKYE 343 Fusobacterium m...
AAN63879     483 --------------------------------------------------------------------------tnDTVA 488 Chinook salmon
YP_001621198 577 --------------------------------------------------------------------------tnDTVA 582 Acholeplasma la...
ZP_03293998  495 nnqnnntnnqnndaannnqsnntqnnnatqnksdvnnknnkkpkkeenpyyteneiksminsitlkiivnrenserVKSA 574 Clostridium hir...
1UQW_A       362 QFTQQQLAQ-VGIKAQVTax--dAGQRAAEVEGkgqkesgvrXFYTGWsastgeadwaLSPLFasqnwppt--------- 429 Escherichia coli
ZP_03761138  428 KAVKSDLKD-IGFDVDIEll--dQAAYLRQVYMlqd----fdLILSGTggwddpsawdGLAEDmqglp------------ 488 Clostridium asp...
ZP_01216339  372 KALKNMLQR-VGLQLLVTqt-dsKDEWLKTMEHy-------dLTLSTWqsslmdrkniYKSLFad--------------- 427 Psychromonas sp...
ZP_02025864  379 EVIQAALQE-IGINSKIVn---vEDALYQTYKTdsk---qfdLILDIKgtddy-ctfpWSLLFdnrsfdg---------- 440 Eubacterium ven...
A1JJG7       422 QTLTKLLAD-QGVNLKIHvv--dYTQWYQGDAQs-------dMWLGSAnfylplefslFATLYelpllqy---------- 481 Yersinia entero...
ZP_02211897  419 SEVRALLKD-VTFKIIVNk---nNSERVKAATIisn---nleAIGIKTeik----dleDDEMTkaldkkdydlaligcel 487 Clostridium bar...
EEO35103     344 IIVKILPYQ-VDAYYYKIk----SKNFDIALQH---------LVFNKKyprislgkviLYDIYddnl------------- 396 Fusobacterium m...
AAN63879     489 DWVKQTVEAiFGDKFELKlngvsSDALDAAWDNfd-----fdMTFGGWqglnfnpvslMGQVYnsisgaanmlengf--- 560 Chinook salmon
YP_001621198 583 NWVKQTVETiFGDKFELKlngvsSDALDAAWDNfd-----fdMTFGGWqglnfnpvslMGQVYnsisgaanmlengf--- 654 Acholeplasma la...
ZP_03293998  575 NMISENLKT-VGIKSEVVll--dSLGMQKSLANrsydlavtgWQISSVpniteimkaiCPNDAglnerlak--------- 642 Clostridium hir...
1UQW_A       430 --------lfntafysNKQVDDFLAQAlktnDPAEKTRLYKAAQDIIWQe------------------------------ 471 Escherichia coli
ZP_03761138  489 ------------tacnSNELNAALGELstaySEKALTAAWKKAADVAALq------------------------------ 526 Clostridium asp...
ZP_01216339  428 --------------slLAPYLGPLYAAqstlNRDDFFKKLLQQQRVILLf------------------------------ 463 Psychromonas sp...
ZP_02025864  441 ---------qtanfikDDKLQELMEKSl--sTDTHNEDSVNEFETYLDEn------------------------------ 479 Eubacterium ven...
A1JJG7       482 ----------cldeelHQDVELWRNNTl--qMADWSQRLVSQNQFHPLF------------------------------- 518 Yersinia entero...
ZP_02211897  488 pavsdatyiikqlgydDKQLDKYLNAL----QNANSEDEIKSTYKTLQKyv----------------------------- 534 Clostridium bar...
EEO35103     397 -------------ykeINYFENRFEKEe---NLEKREKIFIEGVNEISKk------------------------------ 430 Fusobacterium m...
AAN63879     561 --dtgniqlsielphtKAALQKWVAEFneetASEAQLAAYGRWTAALAKfgdsntysdtldnvykaaastfynvsdvnya 638 Chinook salmon
YP_001621198 655 --dtgniqlsielphtKAALQKWVAEFneetASEAQLAAYGRWTAALAKfgdsntysdtldnvykaaastfynvsdvnya 732 Acholeplasma la...
ZP_03293998  643 --------iqgatseeDIKKIYADIEKycidNALFISIGVKDNYMIVNKr------------------------------ 684 Clostridium hir...
1UQW_A       472 --------------------SPWIPLVVEk--lVSAHSK----NLTGF 493 Escherichia coli
ZP_03761138  527 --------------------VPVVPLARPk--qFLAVSA----DLSGY 548 Clostridium asparagiforme DSM 15981
ZP_01216339  464 --------------------SVDELWGADr---KYAFKN----IFSVN 484 Psychromonas sp. CNPT3
ZP_02025864  480 --------------------AYAYGLFTRa--nYIVAKSg---KVSKF 502 Eubacterium ventriosum ATCC 27560
A1JJG7       519 --------------------HHWLELYGQh--sMRGVRM----NTLGW 540 Yersinia enterocolitica subsp. enterocolitica 8081
ZP_02211897  535 -------------------kEKAIFISFGilddYVVLNG----RLDGE 559 Clostridium bartlettii DSM 16795
EEO35103     431 --------------------LPYIPLEHHs---LYILIN----RALEE 451 Fusobacterium mortiferum ATCC 9817
AAN63879     639 grnddfdritaafeaalldeMMQFSGASLl--sDLCSGAgsrsGLPSV 684 Chinook salmon
YP_001621198 733 grnddfdritaafeaalldeMIAIPLFTSv--sATVYSS----RVKFE 774 Acholeplasma laidlawii PG-8A
ZP_03293998  685 --------------------LKTNSYMNDy--dQYRGIE----MVTPS 706 Clostridium hiranonis DSM 13275
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