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(-) Description

Title :  BENM EFFECTOR BINDING DOMAIN WITH ITS EFFECTOR BENZOATE
 
Authors :  T. Clark, S. Haddad, O. Ezezika, E. Neidle, C. Momany
Date :  30 Nov 05  (Deposition) - 31 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lttr, Lysr-Type Transcriptional Regulator, Inducer Binding Domain, Effector Binding Domain, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. C. Ezezika, S. Haddad, T. J. Clark, E. L. Neidle, C. Momany
Distinct Effector-Binding Sites Enable Synergistic Transcriptional Activation By Benm, A Lysr-Type Regulator.
J. Mol. Biol. V. 367 616 2007
PubMed-ID: 17291527  |  Reference-DOI: 10.1016/J.JMB.2006.09.090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BENM, BENR
    Organism Scientific: ACINETOBACTER BAYLYI
    Organism Taxid: 202950
    Strain: ADP1
    Synonym: BEN AND CAT OPERON TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1BEZ5Ligand/IonBENZOIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:104 , LEU A:105 , ILE A:108 , PHE A:144 , ARG A:160 , ILE A:269 , TYR A:293 , HOH A:1016BINDING SITE FOR RESIDUE BEZ A 1001
2AC2SOFTWARELEU B:104 , ILE B:108 , PHE B:144 , LEU B:159 , ARG B:160 , ILE B:269 , TYR B:293BINDING SITE FOR RESIDUE BEZ B 1002
3AC3SOFTWAREVAL A:97 , SER A:99 , ARG A:146 , ASN A:202 , PHE A:203 , HOH A:1027 , HOH A:1033 , HOH A:1080 , HOH A:1123BINDING SITE FOR RESIDUE BEZ A 1003
4AC4SOFTWAREVAL B:97 , SER B:99 , ARG B:146 , PHE B:203 , HOH B:1016 , HOH B:1027 , HOH B:1047BINDING SITE FOR RESIDUE BEZ B 1004
5AC5SOFTWARELYS B:191 , ILE B:192 , LYS B:220 , ILE B:221 , ASN B:222 , HOH B:1208BINDING SITE FOR RESIDUE BEZ B 1005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F78)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:195 -Pro A:196
2Lys A:200 -Pro A:201
3Tyr B:195 -Pro B:196
4Lys B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F78)

(-) Exons   (0, 0)

(no "Exon" information available for 2F78)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:222
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:222
                                                                                                                                                                                                                                                   304    
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       | -  
           BENM_ACIAD    87 SVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f78 A  87 SVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNWLEHH 308
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306  


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:214
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    
           BENM_ACIAD    90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f78 B  90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2F78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F78)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BENM_ACIAD | O68014)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  2f78
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BENM_ACIAD | O68014: 2f6g 2f6p 2f7a 2f8d 2f97 2h99 2h9b 3k1m 3k1n 3k1p 3m1e 4ihs 4iht

(-) Related Entries Specified in the PDB File

2f6g 2f6p 2f7a 2f7b 2f7c 2f8d 2f97