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(-) Description

Title :  DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. TRIGONAL CRYSTAL FORM
 
Authors :  L. Devesse, I. Smirnova, R. Lonneborg, U. Kapp, P. Brzezinski, G. A. Leo C. Dian
Date :  01 Feb 11  (Deposition) - 20 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription Regulator, Dna-Binding, Transcription, Transcription Factor, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Devesse, I. Smirnova, R. Lonneborg, U. Kapp, P. Brzezinski, G. A. Leonard, C. Dian
Crystal Structures Of Dntr Inducer Binding Domains In Complex With Salicylate Offer Insights Into The Activation Of Lysr-Type Transcriptional Regulators.
Mol. Microbiol. V. 81 354 2011
PubMed-ID: 21692874  |  Reference-DOI: 10.1111/J.1365-2958.2011.07673.X

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: INDUCER BINDING DOMAIN, RESIDUES 90-301
    Mutation: YES
    Organism Scientific: BURKHOLDERIA SP.
    Organism Taxid: 233098
    Strain: DNT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1PEU1Ligand/Ion2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
2SAL2Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1PEU2Ligand/Ion2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
2SAL4Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:104 , ILE A:106 , GLY A:107 , PHE A:167 , HIS A:169 , HIS A:206 , ILE A:273 , HOH A:2180 , HOH A:2181BINDING SITE FOR RESIDUE SAL A1000
2AC2SOFTWAREMET A:90 , SER A:95 , ARG A:97 , GLY A:286 , TRP A:289BINDING SITE FOR RESIDUE SAL A1001
3AC3SOFTWAREILE A:106 , PRO A:234 , ARG A:248 , PHE A:249 , ARG A:252 , PRO A:256 , PHE A:257BINDING SITE FOR RESIDUE PEU A1305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7P)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7P)

(-) 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    
   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:215
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:215
                                                                                                                                                                                                                                             301   
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 |   
         Q7WT50_9BURK    90 FDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA---   -
               SCOP domains d2y7pa_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7p A  90 MDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAHHH 304
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y7P)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7WT50_9BURK | Q7WT50)
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: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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  2y7p
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 Related Entries

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

UniProtKB/TrEMBL
        Q7WT50_9BURK | Q7WT50: 1utb 1uth 2y7k 2y7r 2y7w 2y84 5ae4 5ae5

(-) Related Entries Specified in the PDB File

1utb DNTR FROM BURKHOLDERIA SP. STRAIN DNT
1uth DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE
2y7k DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. MONOCLINIC CRYSTAL FORM
2y7r DNTR INDUCER BINDING DOMAIN
2y7w DNTR INDUCER BINDING DOMAIN
2y84 DNTR INDUCER BINDING DOMAIN