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(-) Description

Title :  CRYSTAL STRUCTURE OF BENM_DBD
 
Authors :  A. Alanazi, C. Momany, E. L. Neidle
Date :  04 Mar 10  (Deposition) - 27 Apr 11  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Whth, Activator, Aromatic Hydrocarbons Catabolism, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Alanazi, E. L. Neidle, C. Momany
Crystal Structure Of The Unbound Lysr-Type Transcriptional Regulator Benm Dna Binding Domain
Acta Crystallogr. , Sect. D 2013
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDNA BINDING DOMAIN
    GeneACIAD1435, BENM, BENR
    Organism ScientificACINETOBACTER SP. ADP1
    Organism Taxid62977
    StrainADP1
    SynonymBEN AND CAT OPERON TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:2 , LEU A:3BINDING SITE FOR RESIDUE NA A 95

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M1E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M1E)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.BENM_ACIAD1-58  1A:1-58
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.BENM_ACIAD1-58  2A:1-58

(-) Exons   (0, 0)

(no "Exon" information available for 3M1E)

(-) Sequences/Alignments

Asymmetric 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    
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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:87
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            BENM_ACIAD    1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIAS 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --HTH_1-3m1eA01 A:3-62                                        -----------------------Ly Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_LYSR  PDB: A:1-58 UniProt: 1-58                       ----------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  3m1e A  1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIAS 87
                                    10        20        30        40        50        60        70        80       

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  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 3M1E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M1E)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | O680142f6g 2f6p 2f78 2f7a 2f8d 2f97 2h99 2h9b 3k1m 3k1n 3k1p 4ihs 4iht

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3M1E)