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(-) Description

Title :  SINGLE MUTANT F111L DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE
 
Authors :  R. Lonneborg, I. Smirova, C. Dian, G. A. Leonard, S. Mcsweeney, P. Brzezinski
Date :  04 Apr 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lttr, Lysr, Dna-Binding, Transcription, Transcription Regulation, Transcriptional Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Lonneborg, I. Smirova, C. Dian, G. A. Leonard, P. Brzezinski
In Vivo And In Vitro Investigation Of Transcriptional Regulation By Dntr.
J. Mol. Biol. V. 372 571 2007
PubMed-ID: 17681542  |  Reference-DOI: 10.1016/J.JMB.2007.06.076

(-) Compounds

Molecule 1 - REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: M15/PREP4
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BURKHOLDERIA CEPACIA
    Organism Taxid: 292
    Strain: STRAIN DNT
    Synonym: DNTR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3SCN12Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL8Ligand/IonGLYCEROL
3SCN24Ligand/IonTHIOCYANATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:107 , HIS A:169 , ILE A:273 , HOH A:2037 , HOH A:2101BINDING SITE FOR RESIDUE SCN A1304
02AC2SOFTWAREGLY B:107 , PHE B:167 , HIS B:169 , GOL B:1307 , HOH B:2100BINDING SITE FOR RESIDUE SCN B1302
03AC3SOFTWAREPRO B:133 , ASN B:134BINDING SITE FOR RESIDUE SCN B1303
04AC4SOFTWAREPHE A:229 , ILE A:230 , ILE A:232 , GLY A:233 , PHE A:249 , HOH A:2102BINDING SITE FOR RESIDUE SCN A1305
05AC5SOFTWAREARG A:164 , ARG A:291BINDING SITE FOR RESIDUE SCN A1306
06AC6SOFTWAREPHE A:161 , HOH A:2045 , GLN B:292BINDING SITE FOR RESIDUE SCN A1307
07AC7SOFTWAREVAL B:199 , HIS B:206 , ASP B:210 , ARG B:220 , HOH B:2054BINDING SITE FOR RESIDUE SCN B1304
08AC8SOFTWARETRP B:277 , ARG B:291 , GLN B:292BINDING SITE FOR RESIDUE SCN B1305
09AC9SOFTWAREARG A:220 , HOH A:2103BINDING SITE FOR RESIDUE SCN A1308
10BC1SOFTWARELEU A:212 , ALA A:216 , ILE A:218 , LYS A:267BINDING SITE FOR RESIDUE SCN A1309
11BC2SOFTWAREARG A:165 , HOH A:2104 , PHE B:93 , ARG B:122 , TRP B:289 , HOH B:2024BINDING SITE FOR RESIDUE SCN A1310
12BC3SOFTWAREARG A:165 , PHE B:90BINDING SITE FOR RESIDUE SCN A1311
13BC4SOFTWAREASP A:105 , ARG A:132 , HIS A:228 , HOH A:2012 , HOH A:2105 , ASP B:105 , ARG B:132 , HIS B:228 , HOH B:2018BINDING SITE FOR RESIDUE GOL A1312
14BC5SOFTWAREMET A:116 , ALA A:120 , GLU B:195 , ARG B:223 , THR B:239 , ASP B:240 , HOH B:2101BINDING SITE FOR RESIDUE GOL B1306
15BC6SOFTWAREGLU A:195 , ARG A:223 , THR A:239 , ASP A:240 , LEU A:241 , HOH A:2106 , MET B:116 , ALA B:120BINDING SITE FOR RESIDUE GOL A1313
16BC7SOFTWARETHR B:104 , THR B:204 , GLY B:205 , HIS B:206 , ILE B:273 , SCN B:1302 , ACT B:1308 , HOH B:2102BINDING SITE FOR RESIDUE GOL B1307
17BC8SOFTWAREGLY B:152 , LEU B:153 , LEU B:154 , ASN B:203 , GOL B:1307BINDING SITE FOR RESIDUE ACT B1308

(-) SS Bonds  (0, 0)

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

(-) 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 2UYF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYF)

(-) 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 Q8VUD7_BURCE | Q8VUD7 from UniProtKB/TrEMBL  Length:301

    Alignment length:215
                                                                                                                                                                                                                                              301  
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  |  
         Q8VUD7_BURCE    89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA--   -
               SCOP domains d2uyfa_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains 2uyfA01 A:89-170,A:270-303 Periplasmic binding protein-like II                    2uyfA02 A:171-269 Periplasmic binding protein-like II                                              2uyfA01 A:89-170,A:270-303         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........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
                 2uyf A  89 SFDPFASTRTFNLAMTDIGEMYLMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAHH 303
                                    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:226
 aligned with Q8VUD7_BURCE | Q8VUD7 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      
         Q8VUD7_BURCE    76 ALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
               SCOP domains d2uyfb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyfB01 B:76-170,B:270-301 Periplasmic binding protein-like II                                 2uyfB02 B:171-269 Periplasmic binding protein-like II                                              2uyfB01 B:76-170,B:270-301       CATH domains
           Pfam domains (1) ------------------LysR_substrate-2uyfB01 B:94-299                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) ------------------LysR_substrate-2uyfB02 B:94-299                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author ..hhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee.....hhhhhhhhhhhh....eeeeee....hhhhhhhhh...eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyf B  76 ALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYLMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 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 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   (Q8VUD7_BURCE | Q8VUD7)
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
        Q8VUD7_BURCE | Q8VUD7: 2uye

(-) 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
2uye DOUBLE MUTANT Y110S,F111V DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE