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(-) Description

Title :  CRYSTAL STRUCTURE OF TTHA0167, A TRANSCRIPTIONAL REGULATOR, TETR/ACRR FAMILY FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Agari, K. Sakamoto, K. Agari, S. Kuramitsu, A. Shinkai
Date :  04 Jul 12  (Deposition) - 27 Feb 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Turn-Helix, Transcriptional Regulator, Dna Binding, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Agari, K. Sakamoto, K. Yutani, S. Kuramitsu, A. Shinkai
Structure And Function Of A Tetr Family Transcriptional Regulator, Sbtr, From Thermus Thermophilus Hb8
Proteins V. 81 1166 2013
PubMed-ID: 23408580  |  Reference-DOI: 10.1002/PROT.24266

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (TETR/ACRR FAMILY)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-189
    Gene: TTHA0167
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: TTHA0167

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3VUQ)

(-) Sites  (0, 0)

(no "Site" information available for 3VUQ)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:164 -B:164
2C:164 -D:164

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VUQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VUQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VUQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3VUQ)

(-) 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:178
 aligned with Q5SLX6_THET8 | Q5SLX6 from UniProtKB/TrEMBL  Length:189

    Alignment length:180
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
         Q5SLX6_THET8    10 AGVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 189
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh......--.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vuq A   8 AGVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPS--VEAYLEHLMEVLRKGVEP 187
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  |    177       187
                                                                                                                                                                                         167  |                 
                                                                                                                                                                                            170                 


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q5SLX6_THET8 | Q5SLX6 from UniProtKB/TrEMBL  Length:189

    Alignment length:180
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
         Q5SLX6_THET8    10 AGVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 189
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..----..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vuq B   8 AGVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCT----VEAYLEHLMEVLRKGVEP 187
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       | -  |    177       187
                                                                                                                                                                                       165  170                 


Chain C from PDB  Type:PROTEIN  Length:179
 aligned with Q5SLX6_THET8 | Q5SLX6 from UniProtKB/TrEMBL  Length:189

    Alignment length:179
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         Q5SLX6_THET8    11 GVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 189
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vuq C   9 GVKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 187
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178         


Chain D from PDB  Type:PROTEIN  Length:178
 aligned with Q5SLX6_THET8 | Q5SLX6 from UniProtKB/TrEMBL  Length:189

    Alignment length:178
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
         Q5SLX6_THET8    12 VKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 189
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vuq D  10 VKDKKRAILEATLAVLRERGLSGLKMEEVARRAEVGKGTIYLYFRDKRDLLKALVEERTWAFYREVEEVVRRKAPFFVRLEEVLRRRLAWVQEWRGLWAAVAREAMDDPTPWLKGLHEHYLRLLEELLRSGQSEGAVRTGLSPRATAAVIAAMGCTPSLEVEAYLEHLMEVLRKGVEP 187
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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  (0, 0)

(no "SCOP Domain" information available for 3VUQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VUQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VUQ)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SLX6_THET8 | Q5SLX6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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