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(-) Description

Title :  BENM EFFECTOR-BINDING DOMAIN CRYSTALLIZED FROM HIGH PH CONDITIONS
 
Authors :  O. C. Ezezika, S. Haddad, E. L. Neidle, C. Momany
Date :  02 Dec 05  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Benm, Lttr, Lysr-Type Transcriptional Regulator, Tetramerization, Effector Binding Domain, Inducer Binding Domain, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. C. Ezezika, S. Haddad, E. L. Neidle, C. Momany
Oligomerization Of Benm, A Lysr-Type Transcriptional Regulator: Structural Basis For The Aggregation Of Proteins In This Family.
Acta Crystallogr. , Sect. F V. 63 361 2007
PubMed-ID: 17565172  |  Reference-DOI: 10.1107/S1744309107019185
(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
    Expression System Plasmid: PET21B
    Expression System Strain: DE3 (BL21)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BENM
    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  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1BEZ3Ligand/IonBENZOIC ACID
2GOL6Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:90 , ILE A:92 , ASP A:141 , ARG A:274 , GLU A:277 , SER A:279 , GLU B:278BINDING SITE FOR RESIDUE PO4 B 1004
02AC2SOFTWAREVAL A:97 , SER A:99 , ARG A:146 , LEU A:147 , ASN A:202 , PHE A:203 , HIS A:206 , HOH A:1014 , HOH A:1045BINDING SITE FOR RESIDUE BEZ A 1001
03AC3SOFTWARELEU A:104 , LEU A:105 , ILE A:108 , PHE A:144 , ARG A:160 , ILE A:269 , TYR A:293BINDING SITE FOR RESIDUE BEZ A 1002
04AC4SOFTWARELEU B:104 , LEU B:105 , ILE B:108 , PHE B:144 , LEU B:159 , ARG B:160 , ILE B:269 , TYR B:293BINDING SITE FOR RESIDUE BEZ B 1003
05AC5SOFTWARETYR A:124 , ARG A:139 , HOH A:1184BINDING SITE FOR RESIDUE GOL A 1005
06AC6SOFTWARELYS B:155 , THR B:157 , TYR B:286 , ASN B:303 , TRP B:304 , LEU B:305 , GLU B:306 , HOH B:1227BINDING SITE FOR RESIDUE GOL B 1006
07AC7SOFTWARETYR B:124 , ARG B:139 , HOH B:1171 , HOH B:1217BINDING SITE FOR RESIDUE GOL B 1007
08AC8SOFTWARELYS A:155 , THR A:157 , TYR A:286 , ASN A:303 , TRP A:304 , LEU A:305 , GLU A:306 , HOH A:1116BINDING SITE FOR RESIDUE GOL A 1008
09AC9SOFTWAREGLY A:98 , GLU A:125 , SER A:198 , HOH A:1045 , HOH A:1237BINDING SITE FOR RESIDUE GOL A 1009
10BC1SOFTWARETHR A:132 , LYS A:148 , ILE A:149 , SER A:150 , ASP A:151 , ASN A:185 , HIS A:214BINDING SITE FOR RESIDUE GOL A 1010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F8D)

(-) 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 2F8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F8D)

(-) Exons   (0, 0)

(no "Exon" information available for 2F8D)

(-) 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:221
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:221
                                                                                                                                                                                                                                                 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....hhhhhh...eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f8d A  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNWLEHHH 309
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308 


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:218
                                                                                                                                                                                                                                                 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....hhhhhh...eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhh...eeeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f8d B  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNWLE 306
                                    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 2F8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F8D)

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

(-) Related Entries Specified in the PDB File

2f6g 2f6p 2f78 2f7a 2f7b 2f7c 2f97