PDBsum entry 3fms

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Transcription regulator PDB id
Protein chain
209 a.a. *
ACT ×2
Waters ×81
* Residue conservation analysis
PDB id:
Name: Transcription regulator
Title: Crystal structure of tm0439, a gntr transcriptional regulato
Structure: Transcriptional regulator, gntr family. Chain: a. Engineered: yes. Mutation: yes
Source: Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8 / dsm 3109 / jcm 10099. Gene: tm_0439. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.161     R-free:   0.228
Authors: M.Zheng,D.R.Cooper,M.Yu,L-W.Hung,U.Derewenda,Z.S.Derewenda,I Center For Structure And Function Innovation (Isfi)
Key ref:
M.Zheng et al. (2009). Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Acta Crystallogr D Biol Crystallogr, 65, 356-365. PubMed id: 19307717 DOI: 10.1107/S0907444909004727
22-Dec-08     Release date:   10-Feb-09    
Supersedes: 3dbw
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9WYS0  (Q9WYS0_THEMA) -  GntR family transcriptional regulator
214 a.a.
209 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1107/S0907444909004727 Acta Crystallogr D Biol Crystallogr 65:356-365 (2009)
PubMed id: 19307717  
Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains.
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.
The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-alpha-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.
  Selected figure(s)  
Figure 4.
Figure 4 The dimerization interfaces of the FCD and FadR_C domains. For TM0439, two complete FCD domains are shown, with one monomer colored as in Fig. 3-. Residues described in the text are represented as sticks. For the other structures only the helices that participate in dimerization are shown.
Figure 5.
Figure 5 Metal-binding sites of TM0439 (PDB code 3fms ), CGL2915 (2di3 ) and PS5454 (3c7j ). An OMIT map contoured at 5 is shown for TM0439. This was generated by deleting the metal and acetate and truncating the histidines back to the C^ atoms, shaking the coordinates to yield an r.m.s.d. of 0.3 Å and performing a round of refinement in phexix.refine.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 356-365) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20208147 D.R.Cooper, K.Grelewska, C.Y.Kim, A.Joachimiak, and Z.S.Derewenda (2010).
The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 219-224.
PDB code: 3gor
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