Conserved Protein Domain Family
PBP1_arabinose_binding

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cd01540: PBP1_arabinose_binding 
Click on image for an interactive view with Cn3D
Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily
Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Statistics
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PSSM-Id: 107253
View PSSM: cd01540
Aligned: 10 rows
Threshold Bit Score: 382.927
Threshold Setting Gi: 149902726
Created: 1-Jul-2004
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand binding
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:5ABP_A; Escherichia coli arabinose-binding protein binds D-galactose, contacts calculated at 3.5 A.
    View structure with Cn3D
  • Citation:PMID 2818726

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
5ABP_A         4 KLGFLVKqpeEPWFQTEWKFADKAGkd-lGFEVIKIAvp-dgEKTLNAIDSLAA-SGAKGFVICTPDPKLGSaIVAKARG 80
1ABE_A         4 KLGFLVKqpeEPWFQTEWKFADKAGkd-lGFEVIKIAvp-dgEKTLNAIDSLAA-SGAKGFVICTPDPKLGSaIVAKARG 80
gi 15140363   27 KIGFIVKqpeEPWFQDEWKFADEAAke-kGFTLVKIGaq-dgEKVQSAIDNLGA-QGAQGFIICTPDVKLGPgIVAKAAA 103
gi 17429780   32 KIGFLVKqpeEPWFQDEWRFADQAAke-kGFKLVKIGvp-sgGEVLTAIDNLGA-QHAQGFVICVPDVKLGPaVVAKARQ 108
gi 91796237   36 KIGFIVKkpeQAWFINEQDAATQLGee-kGFEVVRLSge-dgQEVLSAIDNLHS-QGAEGFVICPPDVRLGPaIMNRAEQ 112
gi 77968782   38 KIGFLVKmpeQAWFINEQNAASALGqk-eNFSVVKIGtp-dgEKVLAAIDNLGS-QGAQGFVICAPDVRLGPaIAARAKR 114
gi 95102051   35 KIGFLVKmpeQAWFINEQNAASALGqk-eNFSVVKIGtp-dgEKVLAAIDNLGS-QGAQGFVICAPDVRLGPaIAARAKR 111
gi 28853072   33 KIGFLVKqaeEPWFQTEWAFAEKAGke-hGFTVLKIAvp-dgEKTLSAIDSLAA-NGAKGFVICPPDVSLGPaIVAKAKA 109
gi 13475901   29 KIGYINKmgeHPWFVAEVGGAKKAAea-aGATFVSQDvqfdsNLTITTFDTMVG-DGVKGIAIVVPDKALGPvIAEKAKA 106
gi 149902726  35 VIAVIYKtldEAWFQEESEAAKNKAlamgAKDVITIDak-mnPDVYLSALDNLItQKVDGILICVPDQKLSKiTIDRCKK 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                #                                                                #      
5ABP_A        81 YDMKVIAVDDQFvnakgkpmdtVPLVMMAATKIGERQGQELYkemqk---rgwdvKESAVMAITAneldtARRRTTGSMD 157
1ABE_A        81 YDMKVIAVDDQFvnakgkpmdtVPLVMMAATKIGERQGQELYkemqk---rgwdvKESAVMAITAneldtARRRTTGSMD 157
gi 15140363  104 NDLKLMTVDDRLvnadgspiedVPHMGISATKIGEAVGEAIVaeikk---rgwdmKEVGAIRVSYdqlptAVDRVEGALS 180
gi 17429780  109 NNLKLMTVDDRLvdgggkpieaVPHMGISATRIGEQVGEAIAqemkk---rgwnpSEVGAIRIAYdqlptARERTDGAVA 185
gi 91796237  113 YGMKVVTVDDRFvggdgepmeeVPHLGMSGYKIGEQVGNAIAeemer---rgwdpEEVAALRITNyelptAKERTDGATA 189
gi 77968782  115 YNMKFVTVDDQLvdstgkplpnVPHLGMSATKIGNQVGQAIAdemkr---rgwkpEEVGALRITNyelptAKLRTDGATQ 191
gi 95102051  112 YNMKFVTVDDQLvdstgkplpnVPHLGMSATKIGNQVGQAISdemkr---rgwkpEEVGALRITNyelptAKLRTDGATQ 188
gi 28853072  110 LGLKVMAVDDRFvdakgnfmedVPYLGMAAFEVGQKQGAAMAteaknrkwdeggwKGTYAIINTYneldtGKKRTDGSVK 189
gi 13475901  107 AKIPLVAVDDDIyyqd---gtqVPYVGMNAYNIGARVGEELAklyka---dgwagKEVRIASIEDrkadtCMQRNKGAEE 180
gi 149902726 114 SNIAVIACDDPLtdde--gnyiAPFVGIDSNQIGRDMTSLMVdylekn-nklsdpNSSGLLLMSMdsvssCIPRTEGQLE 190
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                         ##                          #  
5ABP_A       158 ALka--agFPEKQIYQVPTKSndiPGAFDAANSMLVqhp-evkHWLIVGMNDSTVLGGVRATEGQGFkaadIIGIGINGV 234
1ABE_A       158 ALka--agFPEKQIYQVPTKSndiPGAFDAANSMLVqhp-evkHWLIVGMNDSTVLGGVRATEGQGFkaadIIGIGINGV 234
gi 15140363  181 VLka--ngFPEANVFDAPQAKtdtEAALNAATVVLNkna-gikKWVAVGLNDEAVLGAVRATETVGIpadsMIGIGIGGA 257
gi 17429780  186 ALak--agFPAANVLTSPQAKtdtEAAFNAADITLTknp-rfkHWIAFGLNDEAVLGAVRAAEGHGIkaadIIGVGIGGS 262
gi 91796237  190 ALld--sgFKEANIFDAPQQNtdtSSAFAAASPVFSkrs-dfeHWVIYALNEESVLGGVRASEQYGLdpdqVIGVGINGS 266
gi 77968782  192 ALla--ngFRKENIFDAPQKTtddEGGFSAAAPVLArhp-nvkKWVVYALNEETVLGAVRATEQLHIpaadVIGVGINGA 268
gi 95102051  189 ALla--ngFRKENIFDAPQKTtddEGGFSAAAPVLArhp-nvkKWVVYALNEETVLGAVRATEQLHIpaadVIGVGINGA 265
gi 28853072  190 ALee--agLPKDHILFTAQKTldvPGSMDATNSALPklpgdakNLIIGGMNDNTVLGGVRATASNGFsaknVIGIGINGT 267
gi 13475901  181 AFlkavpdFKPANILRVPYDNt-mVNAIDVMTTTLTanp-gvtNWIFYSCNDDGVLGAARALENAGYaadqGMGIGIDGS 258
gi 149902726 191 TFkdrlpsFPRENIFQAEYNGq-sEKSFYSAASTITsnk-nikNWFVMSANEAGTIGAIKALDQSGLae-nAVAVGVGGY 267
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                    
5ABP_A       235 davsel-skaqaTGFYGSLLPSPDVHGYKSSEMLYnwvakdvepPKFTEVTDVVLITRDN 293
1ABE_A       235 davsel-skaqaTGFYGSLLPSPDVHGYKSSEMLYnwvakdvepPKFTEVTDVVLITRDN 293
gi 15140363  258 dsainefkkpsaTGFFGTVIISPKRHGYETALNMYewia-ngkePEKLILTAGQLALRDN 316
gi 17429780  263 qsalnefakpekTGFFGTVLISPKRHGYETSMNMYswit-askaPEPLILTSGRLMTREN 321
gi 91796237  267 gaafaefsretpTGFYGTVAVSSTMHGRQTADNLYqwit-egekPPANTETTGKLMTRDN 325
gi 77968782  269 geafaefqkkepTGFYGTIAVSSTNHGKDSTQNLVdwir-ngktPAPDTQTSGKLMTRAN 327
gi 95102051  266 geafaefqkkepTGFYGTIAVSSTNHGKDSTQNLVewir-dgktPPADTQTSGKLMTRAN 324
gi 28853072  268 daide--lkkkeSGFFGSMLPSPDKEGYNTALYMYkwvtegvepPKYTAMDDVTLITRAN 325
gi 13475901  259 raceaf-gsgkpSAFRGTMWLNSANHGALAVKILLasik-dgtkLPVQSFTDPEYITAGN 316
gi 149902726 268 vakde--fqkqnSPLIASAYISATEVGEIAAQELMenll-lnknIPDKYLVKDKVITKDN 324

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