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(-) Description

Title :  CRYSTAL STRUCTURE OF TM0439, A GNTR TRANSCRIPTIONAL REGULATOR
 
Authors :  M. Zheng, D. R. Cooper, M. Yu, L-W. Hung, U. Derewenda, Z. S. Derewenda, I Center For Structure And Function Innovation (Isfi)
Date :  22 Dec 08  (Deposition) - 10 Feb 09  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gntr Family, Transcriptional Regulator, Structural Genomics, Surface Entropy Reduction, Psi-2, Protein Structure Initiative, Integrated Center For Structure And Function Innovation, Isfi, Dna-Binding, Transcription Regulation, Transcription Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zheng, D. R. Cooper, N. E. Grossoehme, M. Yu, L. W. Hung, M. Cieslik, U. Derewenda, S. A. Lesley, I. A. Wilson, D. P. Giedroc, Z. S. Derewenda
Structure Of Thermotoga Maritima Tm0439: Implications For The Mechanism Of Bacterial Gntr Transcription Regulators With Zn2+-Binding Fcd Domains.
Acta Crystallogr. , Sect. D V. 65 356 2009
PubMed-ID: 19307717  |  Reference-DOI: 10.1107/S0907444909004727

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM_0439
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Strain: MSB8 / DSM 3109 / JCM 10099

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:130 , HIS A:134 , HIS A:174 , HIS A:196 , ACT A:302BINDING SITE FOR RESIDUE NI A 301
2AC2SOFTWAREARG A:86 , ASP A:130 , HIS A:134 , HIS A:196 , VAL A:200 , HOH A:230 , HOH A:243 , NI A:301BINDING SITE FOR RESIDUE ACT A 302
3AC3SOFTWAREPRO A:65 , ARG A:66BINDING SITE FOR RESIDUE ACT A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FMS)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FMS)

(-) 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:209
 aligned with Q9WYS0_THEMA | Q9WYS0 from UniProtKB/TrEMBL  Length:214

    Alignment length:209
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
         Q9WYS0_THEMA     6 VDLVRTKVYNLLKEMILNHELKLGEKLNVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEKFIRETIETRIMMEVFCLENYFDKIAGSEELLEIKGEIDDVEKSAKREIFDDSDERLHKLFIRASGNELIISLYEKIWDRIDLVRHLNERYVVSNREHKELIERIISGDKEGAIEKLKEHLKNVEAETIKNLYTYERS 214
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fms A   6 VDLVRTKVYNLLKEmILNHELKLGEKLNVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEKFIRETIETRImmEVFCLENYFDKIAGSEELLEIKGEIDDVAASAAREIFDDSDERLHKLFIRASGNELIISLYEKIWDRIDLVRHLNERYVVSNREHKELIERIISGDKEGAIEKLKEHLKNVEAETIKNLYTYERS 214
                                    15    |   25        35        45        55        65        75        85  ||    95       105       115       125       135       145       155       165       175       185       195       205         
                                         20-MSE                                                              88-MSE                                                                                                                          
                                                                                                              89-MSE
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  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 3FMS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9WYS0_THEMA | Q9WYS0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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        Q9WYS0_THEMA | Q9WYS0: 3sxk 3sxm 3sxy 3sxz

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