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(-) Description

Title :  DOUBLE MUTANT Y110S,F111V 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  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SCN12Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SCN24Ligand/IonTHIOCYANATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:107 , SER A:110 , PHE A:167 , HIS A:169 , ILE A:273 , HOH A:2035 , HOH A:2109BINDING SITE FOR RESIDUE SCN A1303
02AC2SOFTWAREGLY B:107 , SER B:110 , PHE B:167 , HIS B:169 , ARG B:248 , HOH B:2060BINDING SITE FOR RESIDUE SCN B1302
03AC3SOFTWAREASP B:210 , ARG B:220 , HOH B:2101BINDING SITE FOR RESIDUE SCN B1303
04AC4SOFTWAREARG A:220 , HOH A:2110BINDING SITE FOR RESIDUE SCN A1304
05AC5SOFTWAREMET A:109 , PHE A:229 , ILE A:230 , ILE A:232 , GLY A:233 , PHE A:249 , ILE B:230BINDING SITE FOR RESIDUE SCN A1305
06AC6SOFTWAREALA A:216 , ILE A:218 , LYS A:267 , HOH A:2111BINDING SITE FOR RESIDUE SCN A1306
07AC7SOFTWARETHR A:104 , GLY A:152 , LEU A:153 , GLY A:205 , HIS A:206 , HOH A:2112BINDING SITE FOR RESIDUE SCN A1307
08AC8SOFTWAREARG A:164 , ARG A:291 , GLN A:292 , ARG B:122BINDING SITE FOR RESIDUE SCN A1308
09AC9SOFTWARELEU B:153 , GLY B:205BINDING SITE FOR RESIDUE SCN B1304
10BC1SOFTWAREASP B:105 , ALA B:201 , HIS B:206 , HIS B:228BINDING SITE FOR RESIDUE SCN B1305
11BC2SOFTWAREASP A:105 , ASN A:134BINDING SITE FOR RESIDUE SCN A1309
12BC3SOFTWAREARG A:165 , HOH A:2113 , PHE B:93 , ARG B:122 , TRP B:289 , HOH B:2023BINDING SITE FOR RESIDUE SCN A1310
13BC4SOFTWAREASP A:105 , ARG A:132 , HIS A:228 , HOH A:2114 , ASP B:105 , HIS B:228 , ILE B:230 , HOH B:2018BINDING SITE FOR RESIDUE GOL A1311
14BC5SOFTWAREMET A:116 , ALA A:120 , GLU B:195 , ARG B:223 , THR B:239 , ASP B:240 , LEU B:241 , HOH B:2103BINDING SITE FOR RESIDUE GOL B1306
15BC6SOFTWAREGLU A:195 , ARG A:223 , THR A:239 , ASP A:240 , LEU A:241 , HOH A:2115 , MET B:116 , ALA B:120BINDING SITE FOR RESIDUE GOL A1312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:184 -Pro A:185
2Gly B:136 -Asn B:137
3Ser B:184 -Pro B:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYE)

(-) 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 
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297   | 
         Q8VUD7_BURCE    88 DSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA-   -
               SCOP domains d2uyea_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains 2uyeA01 A:88-170,A:270-302 Periplasmic binding protein-like II                     2uyeA02 A:171-269 Periplasmic binding protein-like II                                              2uyeA01 A:88-170,A:270-302        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
                 2uye A  88 DSFDPFASTRTFNLAMTDIGEMSVMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAH 302
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297     


Chain B from PDB  Type:PROTEIN  Length:225
 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 d2uyeb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyeB01 B:76-170,B:270-301 Periplasmic binding protein-like  II                                2uyeB02 B:171-269 Periplasmic binding protein-like II                                              2uyeB01 B:76-170,B:270-301       CATH domains
           Pfam domains (1) ------------------LysR_substrate-2uyeB01 B:94-299                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) ------------------LysR_substrate-2uyeB02 B:94-299                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee...-.hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhhh...eeeehhhhhhhh....eeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uye B  76 ALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMSVMPPLMEALAQRAPHIQISTLRPN-GNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
                                    85        95       105       115       125        |-|      145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      
                                                                                    134 |                                                                                                                                                                     
                                                                                      136
   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: 2uyf

(-) 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
2uyf SINGLE MUTANT F111L DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE