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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EFFECTOR BINDING DOMAIN OF A BENM VARIANT (BENM R156H/T157S)
 
Authors :  O. C. Ezezika, S. H. Craven, E. L. Neidle, C. Momany
Date :  09 Jun 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lttr, Benm, Transcriptional Activator, Lysr-Type Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Craven, O. C. Ezezika, S. Haddad, R. A. Hall, C. Momany, E. L. Neidl
Inducer Responses Of Benm, A Lysr-Type Transcriptional Regulator From Acinetobacter Baylyi Adp1.
Mol. Microbiol. V. 72 881 2009
PubMed-ID: 19400783  |  Reference-DOI: 10.1111/J.1365-2958.2009.06686.X
(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
    Fragment: EFFECTOR BINDING DOMAIN
    Gene: BENM, BENR
    Mutation: YES
    Organism Scientific: ACINETOBACTER SP.
    Organism Taxid: 62977
    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  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2SO47Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL B:97 , GLY B:127 , THR B:128 , ARG B:146 , LEU B:147 , PRO B:196 , ASN B:202 , PHE B:203 , HOH B:762 , HOH B:830BINDING SITE FOR RESIDUE SO4 B 747
02AC2SOFTWAREALA A:115 , HIS A:116 , PRO A:117 , ASN A:118 , LEU A:119 , TYR A:281 , HOH A:944 , LYS B:129 , HOH B:1058BINDING SITE FOR RESIDUE SO4 A 748
03AC3SOFTWAREHOH A:1007 , LYS B:148 , LYS B:155 , HIS B:156 , HOH B:765 , HOH B:822 , HOH B:898 , HOH B:923 , HOH B:1133BINDING SITE FOR RESIDUE SO4 B 749
04AC4SOFTWAREVAL A:97 , GLY A:127 , THR A:128 , ARG A:146 , LEU A:147 , PRO A:196 , ASN A:202 , PHE A:203 , HOH A:806 , HOH A:833BINDING SITE FOR RESIDUE SO4 A 750
05AC5SOFTWAREHOH A:970 , HIS B:116 , PRO B:117 , ASN B:118 , TYR B:281 , HOH B:1018BINDING SITE FOR RESIDUE SO4 B 751
06AC6SOFTWAREHIS B:206 , ASN B:209 , HOH B:778 , HOH B:823 , HOH B:863 , HOH B:896BINDING SITE FOR RESIDUE SO4 B 752
07AC7SOFTWAREHIS A:206 , ASN A:209 , HOH A:816 , HOH A:835 , HOH A:866 , HOH A:993 , HOH A:1077BINDING SITE FOR RESIDUE SO4 A 753
08AC8SOFTWARELEU A:104 , ARG A:160 , ILE A:269 , HOH A:784 , HOH A:802BINDING SITE FOR RESIDUE CL A 754
09AC9SOFTWARESER B:99 , ARG B:146 , TYR B:195 , GLU B:226 , VAL B:227BINDING SITE FOR RESIDUE CL B 755
10BC1SOFTWAREMET A:177 , ASP A:179 , LYS A:180 , HOH A:1095BINDING SITE FOR RESIDUE CL A 756

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H9B)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:89 -Lys A:90
2Tyr A:195 -Pro A:196
3Lys A:200 -Pro A:201
4Tyr B:195 -Pro B:196
5Lys B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H9B)

(-) Exons   (0, 0)

(no "Exon" information available for 2H9B)

(-) 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:216
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:216
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298      
           BENM_ACIAD    89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh...eeee.......hhhhhhhhhhhh......eeee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h9b A  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298      


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:217
                                                                                                                                                                                                                                                 304 
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     | 
           BENM_ACIAD    89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh...eeee.......hhhhhhhhhhhh......eeee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h9b B  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNWL 305
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
   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 2H9B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H9B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H9B)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        BENM_ACIAD | O68014: 2f6g 2f6p 2f78 2f7a 2f8d 2f97 2h99 3k1m 3k1n 3k1p 3m1e 4ihs 4iht

(-) Related Entries Specified in the PDB File

2f6p BENM-EBD SEMET
2f78 BENM-EBD+BEN
2f7a BENM-EBD + CCM
2f8d BENM-EBD (HIGH PH)
2f97 BENM-EBD (HIGH PH)
2h98
2h99
2h9q