PDBsum entry 3fms

Transcription regulator

PDB id: 3fms

Contents

Protein chain

209 a.a. *

Ligands

ACT ×2

Metals

_NI

Waters ×81

* Residue conservation analysis

PDB id:

3fms

Name:

Transcription regulator

Title:

Crystal structure of tm0439, a gntr transcriptional regulator

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.

Resolution:

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, Integrated 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

Date:

22-Dec-08 Release date: 10-Feb-09

Supersedes:

3dbw

Protein chain

Q9WYS0  (Q9WYS0_THEMA) -  Transcriptional regulator, GntR family from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 214 a.a.

Struc: 209 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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.

ABSTRACT

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.