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(-) Description

Title :  DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. MONOCLINIC CRYSTAL FORM
 
Authors :  L. Devesse, I. Smirnova, R. Lonneborg, U. Kapp, P. Brzezinski, G. A. Leo C. Dian
Date :  31 Jan 11  (Deposition) - 20 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription, Transcription Factor, Lysr Type, Transcription Regulator (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, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: INDUCER-BINDING DOMAIN, RESIDUES 90-301
    Mutation: YES
    Organism Scientific: BURKHOLDERIA SP. DNT
    Organism Taxid: 233098
    Synonym: DNTR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SAL6Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SAL4Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SAL2Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:104 , ILE A:106 , TYR A:110 , PHE A:111 , PHE A:167 , HIS A:169 , HIS A:206 , PRO A:246 , ILE A:273 , HOH A:2071 , HOH A:2072BINDING SITE FOR RESIDUE SAL A1302
2AC2SOFTWARESER A:95 , PRO A:285 , GLY A:286 , TRP A:289BINDING SITE FOR RESIDUE SAL A1303
3AC3SOFTWARETHR B:104 , ILE B:106 , GLY B:107 , TYR B:110 , PHE B:111 , PHE B:167 , HIS B:169 , HIS B:206 , PRO B:246 , ILE B:273 , HOH B:2020 , HOH B:2073BINDING SITE FOR RESIDUE SAL B1304
4AC4SOFTWARESER B:95 , TRP B:289BINDING SITE FOR RESIDUE SAL B1305
5AC5SOFTWARETHR C:104 , ILE C:106 , GLY C:107 , TYR C:110 , PHE C:111 , PHE C:167 , HIS C:169 , HIS C:206 , PRO C:246 , ILE C:273 , HOH C:2024 , HOH C:2085BINDING SITE FOR RESIDUE SAL C1302
6AC6SOFTWARETHR D:104 , ILE D:106 , GLY D:107 , TYR D:110 , PHE D:111 , PHE D:167 , HIS D:169 , HIS D:206 , ILE D:273 , HOH D:2020 , HOH D:2021BINDING SITE FOR RESIDUE SAL D1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:184 -Pro A:185
2Ser B:184 -Pro B:185
3Ser C:184 -Pro C:185
4Ser D:184 -Pro D:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7K)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7K)

(-) 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:211
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:211
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
         Q7WT50_9BURK    91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
               SCOP domains d2y7ka_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee.hhhhh...eeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhh....eeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7k A  91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:213
                                                                                                                                                                                                                                            301  
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300|  
         Q7WT50_9BURK    91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA--   -
               SCOP domains d2y7kb_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee.hhhhh...eeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhhhhhheeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7k B  91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAHH 303
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:212
                                    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 301
               SCOP domains d2y7kc_ C: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee.........eeeeeeee.eeeeee..........hhhhhh..eeeee.....hhhhhhhhhhhh....eeeeee....hhhhhhhhh...eeeehhhhhhhhhhhheeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7k C  90 MDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA 301
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  


Chain D from PDB  Type:PROTEIN  Length:209
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:209
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
         Q7WT50_9BURK    91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
               SCOP domains d2y7kd_ D: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee.hhhhh...eeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhh....eeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7k D  91 DPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y7K)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 1uth 2y7p 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
2y7p DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. TRIGONAL CRYSTAL FORM
2y7r DNTR INDUCER BINDING DOMAIN
2y7w DNTR INDUCER BINDING DOMAIN
2y84 DNTR INDUCER BINDING DOMAIN