1DPP,1DPE


Conserved Protein Domain Family
PBP2_DppA_like

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cd08493: PBP2_DppA_like 
Click on image for an interactive view with Cn3D
The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold.
This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. 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. 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: 173858
View PSSM: cd08493
Aligned: 84 rows
Threshold Bit Score: 465.114
Threshold Setting Gi: 184200663
Created: 5-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:1DPP_A; Escherichia coli dipeptide binding protein (DppA) binds glycyl-L-leucine, contacts at 4 A.
    View structure with Cn3D
  • Citation:PMID 8563629

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
1DPP_A         2 TLVYCSegspegFNPQLftsgTTYDASSVPLYNRLVEFKigtTEVIPG--LAEKWEVsedgkTYTFHLRKgVKWHDnkef 79  Escherichia coli
NP_693372     52 VLVFARggdsesLDPGStt-dGESSRVTRQILESLLDFDkesFEIKPG--LAHDWDIsedglTYTFYLEEgVTFHD---- 124 Oceanobacillus ...
AAB41688      50 TLVFARggdsvsLDYASvt-dGESSRVTKNIYETLIEFDrdsFEIGPG--LAHDWEVddsglRFVFHLEEgVKFHD---- 122 Bacillus firmus
YP_002771490  54 QLIIGRgadtkgLDPITqt-dGETFKVTENIMDTLIGFAdgsTELAPS--LAEKWEVtpdglVYTLKLRSgVKFHD---- 126 Brevibacillus b...
YP_359974     38 VFVFAKsgdpvgLDPANvt-dGESIYVTQQIFETLVKYKddnTEVVPG--LAESWETskdglTWTFHLRKgVKFHD---- 110 Carboxydothermu...
YP_832027     77 TFTFGTaaqplgLDPALas-dVESYRITRQVLEGLVGVDq--TTGLPTplLATEWAEsnegrAYTFKLREgVTFQD---- 149 Arthrobacter sp...
YP_001854870  42 TFVLAHaaaptgLDPSRrn-sQETSRISTQILEGLVSADrstGEPAPG--LAESWEIaddkrSVTFTLRDdVRFHD---- 114 Kocuria rhizoph...
ZP_01173039   43 TLVFGRsgdsdaLDPAVtt-eGESFKVTVNIFETLINFGeqdTEIQPG--LATEWEEsedglKHTLKLREgVKFHD---- 115 Bacillus sp. NR...
YP_076144     48 VLVWGRggdsvsLDPIQvt-dGESLKVTHQIYEGLLDYApgsTEVVPV--LATEWEAspdglEWTFKLRQgVKFHD---- 120 Symbiobacterium...
YP_002250575  28 TLVFGRggdsvkLDPINvt-dGESLRVTHQIFDTLVKYKpnnTEVVPS--LAVKWTVskdqkVWTFYLRKgVKFHD---- 100 Dictyoglomus th...
Feature 1                                                                                        
1DPP_A        80 kpTRELNADDVVFSFDRQKNaqnpyhkvsggs-------yeyfegmglpelISEVKKVDDNTVQFVLtrpeaPFLADLAM 152 Escherichia coli
NP_693372    125 --GTDFNAEAVKTNFERWADpnheyaftdegfvyniygtmfggfegdeghvIDEINAVSEHEVEFVLkeplgFFLQNLAM 202 Oceanobacillus ...
AAB41688     123 --GTDFNAEAVKVNFERWADpehkyafldegytysvygtqfggykgdeghvIEEINVLGDYEIEFVLnqplgSFLQNMGM 200 Bacillus firmus
YP_002771490 127 --GTDFNAEAVKYNFERWSDkshpqhspegyeyy---vsqfggykgdathiIKSVEAVDPTTVKFTLnrplaPFLANLAM 201 Brevibacillus b...
YP_359974    111 --GTPFNAEAVKFNFDRWMNknnpyhhgefey--------ygymfggypgvIKEVKVVDEYTVQITLktplaPFLSNLAM 180 Carboxydothermu...
YP_832027    150 --GTRFDAAAVCANFNRWFNfpaslrkqapgtsfk--gvfkayadqaslsiYKGCTAVSAGNVRIDLtqpftGFLQALTL 225 Arthrobacter sp...
YP_001854870 115 --GTELDAAAVKANFDKWRAqaesgepwahrsafa-ttfrhgytdpmvstsYAGVEVRDERTVVLTLtrpysPLLSALTQ 191 Kocuria rhizoph...
ZP_01173039  116 --GTDFNAEAVVFNFNRWKAgnkeefyy---------------yasqfgdvLTEVKAVDDYTVEFTLsrpiaPFLKNLAM 178 Bacillus sp. NR...
YP_076144    121 --GTDFNAEAVKINFDRWRNtsdplhvggefpy-----ysymfggfdeasnIQDVIVVDDYTVKFVLkniqaSFLQDIAM 193 Symbiobacterium...
YP_002250575 101 --GTPFNAQAVKFNFDRWRDpknpyhfggefe-------ywgymfggfpgiVKSVDVIDDYTVKITLtkplaPFLSNLAM 171 Dictyoglomus th...
Feature 1                                                                                        
1DPP_A       153 dfasilskeyada--------mmkagtpekldlnPIGTGPFQLQQYQKdSRIRYKAFDGYWg-tKPQIDTLVFSItpdas 223 Escherichia coli
NP_693372    203 syfaitspaal-------------eeygpditenPVGTGPFKFNNWSKnDSIVLDKFEDYRvegLPKLDQVIFQVipdns 269 Oceanobacillus ...
AAB41688     201 syfaitspqaf-------------eehgsainenPVGTGPFKFVSWSRdDSIILEKNEDYWkegLPKLDRVIFQVipdns 267 Bacillus firmus
YP_002771490 202 spfaigspeal-------------kkdvkkfnehPIGTGPFKFVEWKRnDTITLEKNPDYWstgYPKLDKLVFKVipent 268 Brevibacillus b...
YP_359974    181 psfaisspeai-------------kkygqdyfkhPVGTGPFKFVEWKKdDRVVLERFDEYWg-gKANFAKVIFRTipdns 246 Carboxydothermu...
YP_832027    226 pafaissptamaaqkadslsqtrdgqpvsayalhPVGTGPFSFAAWQD-SSVKLVSNKDYWg-dRGQIGTINFVTydhpq 303 Arthrobacter sp...
YP_001854870 192 pafgiaspgs---------------ieagtedehPVGTGPFRFDSASG-TTVKLVSNERYWg-dLGQVGSLEMRVipdae 254 Kocuria rhizoph...
ZP_01173039  179 spfgiaspaav-------------ekagdkftdnPVGTGPFKFKEWKRnDRVVIEKNPDYWqegLPKLDSVIFRVipens 245 Bacillus sp. NR...
YP_076144    194 vpfaiaspkal-------------qenperlndhPVGTGPFRFVSWTKgDRIVLEANPDYWg-gKPAIDRLIYRSipdnn 259 Symbiobacterium...
YP_002250575 172 pcfaiasptai-------------kkykedffknPVGTGPFKFVSWIKgDKIVLEANKNYWd-gAPYLDKIIFRSipdns 237 Dictyoglomus th...
Feature 1                                                                                        
1DPP_A       224 vryaKLQKNe---cQVMPypnpadiarmkqdksiNLM-EMPGlnVGYLSYNvqkkpldDVKVRQALTYAVNKDAIIKAVY 299 Escherichia coli
NP_693372    270 arliALQSGe---iDMMDglnpddaaglegeegiELL-TRGEnnFGYVGFHtqkepvdQKEVRQAINYAINKQAIADALY 345 Oceanobacillus ...
AAB41688     268 arltALRSGq---iDIMDglnpddvaqiegddslQVF-ERTTnnIGYLGFHvdkepfnDPVVRRAFNHAIDKEGLIAILY 343 Bacillus firmus
YP_002771490 269 arltALASGe---iDLMDglntddipavkdnkdlQLF-LRPTnnIGYIGFNvekkpldNPKVREAIAYAINKPEIVTAFF 344 Brevibacillus b...
YP_359974    247 arlmELKSGn---vDAITdinpddveavkndpnlQLL-LRPSmnVGYLAMNtekkpfdNVKVRQAINYAINKKALVDAFY 322 Carboxydothermu...
YP_832027    304 srlqALLDGkidgyDAVTvgnfdq----lvkrgqQII-QRDPfsVMYLGMNqevpilqNIKVRQAIEMAVDKETLIRRFF 378 Arthrobacter sp...
YP_001854870 255 vrcaALLGGevdayDLVGlddfap----laregvQVLyRDPYa-VSYLGLNqrvpalrDVSVRRAVAAAIDRRALATSLF 329 Kocuria rhizoph...
ZP_01173039  246 arlnALSTGe---vDLIDgvsfsdvgqiegnadlQLF-DRPSmnVGYLGLTntrgplkDKKVRQALNYAVDKQALIDAFY 321 Bacillus sp. NR...
YP_076144    260 arlvALQAGe---lDVMDgvepaflptiqatgqfDII-ERPPmnIGYLAFNtqkppfdNVLIRRAINHAINKEELNTAFY 335 Symbiobacterium...
YP_002250575 238 arfmELEAGt---vDIIDginpedvervkqnknlQLF-IRPSlnVCYIAMNmdkkpfdDIRVRLAINYAIDKKAIVDAYY 313 Dictyoglomus th...
Feature 1                                                                                        
1DPP_A       300 q-GAGVSAknliPPTMWGYNDDVqdytYDPEKAKALLKEAGLek--gfSIDLWAMpvqr-pynPNARRMAEMIQADWAKV 375 Escherichia coli
NP_693372    346 a-GYATTAknplPPSYLGYNDGVegyeYNPDRARELLEEAGHad--glEIELMISptar-pymPDPETVAQIVQENLSEV 421 Oceanobacillus ...
AAB41688     344 g-GLAETAkntiPPGYLGYNDAIdeysYDPELAKELLAEAGIed--gfTFDLWTMpvar-pymPDPQRAAEAIQANLADV 419 Bacillus firmus
YP_002771490 345 d-GVGEPAvnpmPKTMWGHNNDIkdreFNLDKAKQLLAEAGHpn--gfKIKFWAMpvpr-pymPEGVKIAEAIQQDLKKI 420 Brevibacillus b...
YP_359974    323 g-GLAKPAknplPPSLWGYNDEIqdyeYDPAKAKALLAEAGYpn--gfTTTLWAMpvar-pymPQPKQIAEAIQKDLEAV 398 Carboxydothermu...
YP_832027    379 idNTAQATqf-vPPKLSGFNNNApslgHDPAKAKALLEEAGYkg---eELKFYYPlnvtrpylPTPEKVYAELSRQLTAV 454 Arthrobacter sp...
YP_001854870 330 pnGTNVADqf-vPARFNVNGEHLqlpgYDPQHAKDLLRGSAYkg---eRLRFCYPrntsrmylQEPERVYAQISAQLTRA 405 Kocuria rhizoph...
ZP_01173039  322 s-GYAEPAknpmPPGIAGYNDEVqdyeYNPEKAKELLKEAGYen--gfEMELWAMpvar-pymPDGQKVAEAIQANFADV 397 Bacillus sp. NR...
YP_076144    336 g-GMGIPAvsplPPSVWGHNPNVpkyeYDPEKAKELLAQAGYgpdnplKTELWAMpvpr-pymPQPERIGVAIQNYLREV 413 Symbiobacterium...
YP_002250575 314 pkGFAMVAknpiPPSLWGYNDKIqdysYDPEKAKKLLAEAGYpn--gfKTTLWAMpvnr-pyiPQPMKVAEAVQSYLKAV 390 Dictyoglomus th...
Feature 1                   #   #              #### #                                            
1DPP_A       376 GVQAKIVty-eWGEYLKRAKDge--hqTVMMGWTGDngDPDNFFATLFscaaseq--gsnyskWCYKPFEDLIQPARAtd 450 Escherichia coli
NP_693372    422 GIELTITsh-eWAPYLELTEQge--hqMYILGWSGTngDPDYFLSSLLhssnig---ssnntfYENSEVDDLLNQAKRav 495 Oceanobacillus ...
AAB41688     420 GITANIVtk-eWATYLEETEQgk--hdVFMLGWSGVngDPDYFFSNLLhgdaip---ggnrsfYSNEEVNELLVQAKTev 493 Bacillus firmus
YP_002771490 421 GVDAEIVtm-eWATYLEKTRLge--qeMFMLGWTGDngDPDNFLAVLLdknnig---snnytrWANEEAHQLMMKAQStp 494 Brevibacillus b...
YP_359974    399 GIKAKIVty-dWATYLKKGENge--hdLYLLGWTGDngDPDNFLYVLLdkdnakkgsasnvafYKNDKVHELLIKAQQes 475 Carboxydothermu...
YP_832027    455 GLNIKPVpvewSDGYLQKVQSpgd-haLHLLGWNGSysDPDNFVGPLFgekt-------gefgYQDPQVFSKIARARGlp 526 Arthrobacter sp...
YP_001854870 406 GFRITPVpvdwEDGYVETATDpgadhaLSLLGWSGSfrDPDSFLGPLLgssq-------arlgCDDAGLSTAVNRAAAma 478 Kocuria rhizoph...
ZP_01173039  398 GVKAKIVsy-eWGTYLDKANKge--adSFLLGWTGDngDADNFLYVLLdqdtig---snnytyYKNQEVHDLLIKAQTlt 471 Bacillus sp. NR...
YP_076144    414 GIEAEIVty-eWGTYLEKTGMge--htMALLGWTGDngDPDNFLYVLLdkdnavtpdagniafYVNDEVHDLLIRARQtt 490 Symbiobacterium...
YP_002250575 391 GIDAEIVty-dWGTYLQKTENge--hdMAFLGWTGDngDPDNFFYVLLdkdnavkgsagniafYRSDELHEILIKAQTis 467 Dictyoglomus th...
Feature 1                                                 
1DPP_A       451 DHNKRVELYKQAQVVMHDQAPALIIAHStvFEPVRKEVKGY 491 Escherichia coli
NP_693372    496 DQDERADLYMQAQELISEDSPMVTLVHStpVMAISSNVQNY 536 Oceanobacillus iheyensis HTE831
AAB41688     494 DFDVRAELYEQVQELIHEDAPMVPLVHSipTLAGSSNVKNY 534 Bacillus firmus
YP_002771490 495 DQAEREKMYKKVQEIIFKDVPMVPLAHStpALAGKANIVDY 535 Brevibacillus brevis NBRC 100599
YP_359974    476 DQTKRAEYYKEAQVIIHNDAPWVPLVHStpPVAARKSVKNW 516 Carboxydothermus hydrogenoformans Z-2901
YP_832027    527 EGEERTQQYRTINAQIAESVPAVPIAFPisALALSDRVLKY 567 Arthrobacter sp. FB24
YP_001854870 479 QGDPRTASYKALNDRVSEVVPAVPLSHPvsAVAVSSRVVNF 519 Kocuria rhizophila DC2201
ZP_01173039  472 DQAEREELYKQAQLIIKDDAPWIPLVHSnpVLAGKADITGF 512 Bacillus sp. NRRL B-14911
YP_076144    491 DQAERTRLYEEAQVKIMEDAPWVPLMHTrvPIAVRKGITGY 531 Symbiobacterium thermophilum IAM 14863
YP_002250575 468 NQKERAKLYEKACEIVHRDVPWVILAHTmpPLAGKKTVHNY 508 Dictyoglomus thermophilum H-6-12

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