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(-) Description

Title :  DNTR FROM BURKHOLDERIA SP. STRAIN DNT
 
Authors :  I. A. Smirnova, C. Dian, G. A. Leonard, S. Mcsweeney, D. Birse, P. Brzezinski
Date :  05 Dec 03  (Deposition) - 01 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transcription Regulation, Lysr, Transcriptional Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Smirnova, C. Dian, G. A. Leonard, S. Mcsweeney, D. Birse, P. Brzezinski
Development Of A Bacterial Biosensor For Nitrotoluenes: The Crystal Structure Of The Transcriptional Regulator Dntr
J. Mol. Biol. V. 340 405 2004
PubMed-ID: 15210343  |  Reference-DOI: 10.1016/J.JMB.2004.04.071

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BURKHOLDERIA SP.
    Organism Taxid: 233098
    Strain: DNT
 
Molecule 2 - LYSR-TYPE REGULATORY PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BURKHOLDERIA SP.
    Organism Taxid: 233098
    Strain: DNT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL10Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:104 , ILE A:106 , HIS A:169 , HIS A:206 , ILE A:273BINDING SITE FOR RESIDUE ACT A1305
2AC2SOFTWARETHR B:104 , ILE B:106 , GLY B:107 , HIS B:169 , HIS B:206 , ILE B:273 , HOH B:2054BINDING SITE FOR RESIDUE ACT B1305
3AC3SOFTWAREASP A:105 , ARG A:132 , HIS A:228 , HOH A:2056 , HOH A:2057 , HOH A:2058 , ASP B:105 , ARG B:132 , HIS B:228BINDING SITE FOR RESIDUE GOL A1303
4AC4SOFTWAREGLU A:195 , ARG A:223 , THR A:239 , ASP A:240 , LEU A:241 , HOH A:2059 , MET B:116 , ALA B:120BINDING SITE FOR RESIDUE GOL A1304
5AC5SOFTWAREMET A:109 , ILE A:230 , PHE A:257 , HOH A:2044 , MET B:109 , PHE B:229 , ILE B:230 , ILE B:232 , GLY B:233 , PHE B:249 , PHE B:257BINDING SITE FOR RESIDUE GOL B1302
6AC6SOFTWAREMET A:116 , ALA A:120 , GLU B:195 , ARG B:223 , THR B:239 , ASP B:240BINDING SITE FOR RESIDUE GOL B1303
7AC7SOFTWARETYR B:171 , VAL B:199 , HIS B:206 , VAL B:209 , PHE B:229 , THR B:244 , VAL B:245 , PRO B:246 , HOH B:2031 , HOH B:2053BINDING SITE FOR RESIDUE GOL B1304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UTB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:184 -Pro A:185
2Ser B:184 -Pro B:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UTB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UTB)

(-) Exons   (0, 0)

(no "Exon" information available for 1UTB)

(-) 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:214
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:214
                                                                                                                                                                                                                                              301 
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  | 
         Q7WT50_9BURK    89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA-   -
               SCOP domains d1utba_ A: LysR-type regulatory protein DntR                                                                                                                                                                           SCOP domains
               CATH domains 1utbA01 A:89-170,A:270-302 Periplasmic binding protein-like II                    1utbA02 A:171-269 Periplasmic binding protein-like II                                              1utbA01 A:89-170,A:270-302        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1utb A  89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAH 302
                                    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:227
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:227
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
         Q7WT50_9BURK    75 YALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
               SCOP domains d1utbb_ B: LysR-type regulatory protein DntR                                                                                                                                                                                        SCOP domains
               CATH domains 1utbB01 B:75-170,B:270-301 Periplasmic binding protein-like II                                  1utbB02 B:171-269 Periplasmic binding protein-like II                                              1utbB01 B:75-170,B:270-301       CATH domains
           Pfam domains (1) -------------------LysR_substrate-1utbB01 B:94-299                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) -------------------LysR_substrate-1utbB02 B:94-299                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhhh...eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1utb B  75 YALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLSEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPERFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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