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(-) Description

Title :  DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE
 
Authors :  I. A. Smirnova, C. Dian, G. A. Leonard, S. Mcsweeney, D. Birse, P. Brzezinski
Date :  09 Dec 03  (Deposition) - 01 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 17)

Asymmetric/Biological Unit (1, 17)
No.NameCountTypeFull Name
1SCN17Ligand/IonTHIOCYANATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:107 , ILE A:273 , SCN A:1310 , HOH A:2033 , HOH A:2043BINDING SITE FOR RESIDUE SCN A1305
02AC2SOFTWAREARG A:220 , HOH A:2102BINDING SITE FOR RESIDUE SCN A1306
03AC3SOFTWAREMET A:109 , PHE A:229 , ILE A:230 , GLY A:233 , PHE A:249 , ILE B:230BINDING SITE FOR RESIDUE SCN A1307
04AC4SOFTWAREASP A:105 , ASN A:134BINDING SITE FOR RESIDUE SCN A1308
05AC5SOFTWAREALA A:216BINDING SITE FOR RESIDUE SCN A1309
06AC6SOFTWARETHR A:104 , LEU A:153 , GLY A:205 , SCN A:1305 , HOH A:2034BINDING SITE FOR RESIDUE SCN A1310
07AC7SOFTWAREARG A:165 , HOH A:2039 , HOH A:2041 , PHE B:93 , ARG B:122 , TRP B:289BINDING SITE FOR RESIDUE SCN A1311
08AC8SOFTWAREARG A:164 , TRP A:277 , ARG A:291 , GLN A:292BINDING SITE FOR RESIDUE SCN A1312
09AC9SOFTWAREGLN A:163 , PHE B:90BINDING SITE FOR RESIDUE SCN A1313
10BC1SOFTWAREARG A:168 , GLU A:300 , HOH A:2103BINDING SITE FOR RESIDUE SCN A1314
11BC2SOFTWAREGLY A:160 , GLN B:292 , SCN B:1306BINDING SITE FOR RESIDUE SCN A1315
12BC3SOFTWAREGLY B:107 , HIS B:169 , HOH B:2023 , HOH B:2062BINDING SITE FOR RESIDUE SCN B1302
13BC4SOFTWAREARG B:220 , HOH B:2063BINDING SITE FOR RESIDUE SCN B1303
14BC5SOFTWAREARG B:132 , GLY B:134BINDING SITE FOR RESIDUE SCN B1304
15BC6SOFTWARELEU B:153 , LEU B:154BINDING SITE FOR RESIDUE SCN B1305
16BC7SOFTWARESCN A:1315 , TRP B:277 , ARG B:291 , GLN B:292BINDING SITE FOR RESIDUE SCN B1306
17BC8SOFTWAREARG A:223 , ALA B:120 , ALA B:123 , PRO B:124 , ILE B:126 , HOH B:2064BINDING SITE FOR RESIDUE SCN B1307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 1UTH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UTH)

(-) 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:219
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:219
                                                                                                                                                                                                                                                 301   
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     |   
         Q7WT50_9BURK    86 TRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA---   -
               SCOP domains d1utha_ A: LysR-type regulatory protein DntR                                                                                                                                                                                SCOP domains
               CATH domains 1uthA01 A:86-170,A:270-304 Periplasmic binding protein-like II                       1uthA02 A:171-269 Periplasmic binding protein-like II                                              1uthA01 A:86-170,A:270-304          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhh....eeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uth A  86 TRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAHHH 304
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:226
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      
         Q7WT50_9BURK    76 ALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
               SCOP domains d1uthb_ B: LysR-type regulatory protein DntR                                                                                                                                                                                       SCOP domains
               CATH domains 1uthB01 B:76-170,B:270-301 Periplasmic binding protein-like II                                 1uthB02 B:171-269 Periplasmic binding protein-like II                                              1uthB01 B:76-170,B:270-301       CATH domains
           Pfam domains (1) ------------------LysR_substrate-1uthB01 B:94-299                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) ------------------LysR_substrate-1uthB02 B:94-299                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author ....hhhhhh............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
                 1uth B  76 ALNTLETALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPGAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295
   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  (1, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological 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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 Related Entries

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

UniProtKB/TrEMBL
        Q7WT50_9BURK | Q7WT50: 1utb 2y7k 2y7p 2y7r 2y7w 2y84 5ae4 5ae5

(-) Related Entries Specified in the PDB File

1utb DNTR FROM BURKHOLDERIA SP. STRAIN DNT