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(-) Description

Title :  BENM EFFECTOR BINDING DOMAIN- SEMET DERIVATIVE
 
Authors :  T. Clark, S. Haddad, O. Ezezika, E. Neidle, C. Momany
Date :  29 Nov 05  (Deposition) - 31 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , PRO A:117 , ASN A:118 , LEU A:119 , TYR A:281 , LYS B:129BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREVAL 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:676BINDING SITE FOR RESIDUE SO4 B 601
3AC3SOFTWARELEU B:104 , ARG B:160 , TYR B:293 , HOH B:762BINDING SITE FOR RESIDUE ACT B 602
4AC4SOFTWAREHIS B:116 , LEU B:119 , HOH B:665 , HOH B:793BINDING SITE FOR RESIDUE NA B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F6P)

(-) 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 2F6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F6P)

(-) Exons   (0, 0)

(no "Exon" information available for 2F6P)

(-) 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:218
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:218
                                                                                                                                                                                                                                                304   
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    |   
           BENM_ACIAD    90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW---   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhh.....hhhhh....eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6p A  90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEmGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLmVAVHASHPLNQmKDKGVHLNDLIDEKILLYPSSPKPNFSTHVmNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNmEESTYIYSLYETIRQIYAYEGFTEPPNWLEH 307
                                    99       109       119      |129       139       149       159     | 169       179       189       199       209       219       229       239       249       259       269      |279       289       299        
                                                              126-MSE                                165-MSE     177-MSE                        208-MSE                                                             276-MSE                           


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:224
                                                                                                                                                                                                                                                   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 hhh.eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh...eeee.......hhhhhhhhhhhh......eeee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6p B  87 SVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEmGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLmVAVHASHPLNQmKDKGVHLNDLIDEKILLYPSSPKPNFSTHVmNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNmEESTYIYSLYETIRQIYAYEGFTEPPNWLEHHHH 310
                                    96       106       116       126       136       146       156       166       176|      186       196       206 |     216       226       236       246       256       266       276       286       296       306    
                                                                 126-MSE                                165-MSE     177-MSE                        208-MSE                                                             276-MSE
   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 2F6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F6P)

(-) 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 2f78 2f7a 2f8d 2f97 2h99 2h9b 3k1m 3k1n 3k1p 3m1e 4ihs 4iht

(-) Related Entries Specified in the PDB File

2f6g 2f78 2f7a 2f7b 2f7c 2f8d 2f97