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(-) Description

Title :  CRYSTAL STRUCTURE OF TTHA1359, A TRANSCRIPTIONAL REGULATOR, CRP/FNR FAMILY FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Agari, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Nov 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Fnr/Crp Family, Transcriptional Regulator, Thermus Thermophilus, Stationary Phase, Dna-Binding, Transcription Regulation, Winged Helix Dna-Binding Domain, Camp-Binding Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Agari, A. Kashihara, S. Yokoyama, S. Kuramitsu, A. Shinkai
Global Gene Expression Mediated By Thermus Thermophilus Sdrp, A Crp/Fnr Family Transcriptional Regulator
Mol. Microbiol. V. 70 60 2008
PubMed-ID: 18699868  |  Reference-DOI: 10.1111/J.1365-2958.2008.06388.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, FNR/CRP FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB8
    Synonym: TTHA1359

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:108 , GLU A:111 , THR A:115 , GLN A:116 , GLU A:195 , SER A:196BINDING SITE FOR RESIDUE MPD A 301
2AC2SOFTWAREGLU A:42 , GLU A:138 , GLU A:139 , GLY A:178 , LYS A:181 , GLN A:183 , HOH A:404BINDING SITE FOR RESIDUE MPD A 302
3AC3SOFTWAREVAL A:40 , GLY A:44 , GLU A:73 , THR A:163 , ARG A:171 , HOH A:358BINDING SITE FOR RESIDUE MPD A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZCW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CRP_2PS51063 Crp-type HTH domain profile.SDRP_THET8117-189  1A:116-188
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CRP_2PS51063 Crp-type HTH domain profile.SDRP_THET8117-189  2A:116-188

(-) Exons   (0, 0)

(no "Exon" information available for 2ZCW)

(-) 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:194
 aligned with SDRP_THET8 | Q5SIL0 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:194
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    
           SDRP_THET8     6 ETVSFKAGDVILYPGVPGPRDRAYRVLEGLVRLEAVDEEGNALTLRLVRPGGFFGEEALFGQERIYFAEAATDVRLEPLPENPDPELLKDLAQHLSQGLAEAYRRIERLATQRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELAREGYIRSGYGKIQLLDLKGLKELAESRG 199
               SCOP domains d2zcwa2 A:5-116 Transcriptional regulator TTHA1359, N-terminal domain                                           d2zcwa1 A:117-198 Transcriptional regulator TTHA1359, C-terminal domain            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee...........eeeee..eeeeee.....eeeeeee....eehhhhhh......eeee...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: A:116-188 UniProt: 117-189                               ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zcw A   5 ETVSFKAGDVILYPGVPGPRDRAYRVLEGLVRLEAVDEEGNALTLRLVRPGGFFGEEALFGQERIYFAEAATDVRLEPLPENPDPELLKDLAQHLSQGLAEAYRRIERLATQRLKNRmAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELAREGYIRSGYGKIQLLDLKGLKELAESRG 198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
                                                                                                                                               122-MSE
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 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (SDRP_THET8 | Q5SIL0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001216    bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to activate or increase the frequency, rate or extent of transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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