PDBsum entry 2fe3

DNA binding protein

PDB id

2fe3

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Contents

			Protein chains

					141 a.a. *

			Metals

					_ZN ×2

			Waters ×289

* Residue conservation analysis

PDB id:

2fe3

Links

Name:

DNA binding protein

Title:

The crystal structure of bacillus subtilis perr-zn reveals a novel zn(cys)4 structural redox switch

Structure:

Peroxide operon regulator. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.75Å

R-factor:

0.172

R-free:

0.229

Authors:

D.A.K.Traore

Key ref:

D.A.Traoré et al. (2006). Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis. Mol Microbiol, 61, 1211-1219. PubMed id: 16925555

Date:

15-Dec-05

Release date:

19-Dec-06

PROCHECK

	Headers

	References

Protein chains

P71086 (PERR_BACSU) - Peroxide operon regulator from Bacillus subtilis (strain 168)

Seq: Struc:					145 a.a. 141 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Mol Microbiol 61:1211-1219 (2006)
PubMed id: 16925555

Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis.
D.A.Traoré, A.El Ghazouani, S.Ilango, J.Dupuy, L.Jacquamet, J.L.Ferrer, C.Caux-Thang, V.Duarte, J.M.Latour.

ABSTRACT

Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor that binds DNA in the presence of a regulatory metal Mn2+ or Fe2+, mediates the adaptive response to H2O2. This study presents the first crystal structure of apo-PerR-Zn which shows that all four cysteine residues of the protein are involved in zinc co-ordination. The Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer. Sequence alignment of PerR-like proteins supports that this structural site may constitute a distinctive feature of this class of peroxide stress regulators.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21208302

C.Dian, S.Vitale, G.A.Leonard, C.Bahlawane, C.Fauquant, D.Leduc, C.Muller, H.de Reuse, I.Michaud-Soret, and L.Terradot (2011).
The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites.

Mol Microbiol, 79, 1260-1275.

PDB code:

2xig

21383173

J.H.Shin, H.J.Jung, Y.J.An, Y.B.Cho, S.S.Cha, and J.H.Roe (2011).
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur.

Proc Natl Acad Sci U S A, 108, 5045-5050.

21347346

Z.Ouyang, R.K.Deka, and M.V.Norgard (2011).
BosR (BB0647) Controls the RpoN-RpoS Regulatory Pathway and Virulence Expression in Borrelia burgdorferi by a Novel DNA-Binding Mechanism.

PLoS Pathog, 7, e1001272.

20094649

V.Duarte, and J.M.Latour (2010).
PerR vs OhrR: selective peroxide sensing in Bacillus subtilis.

Mol Biosyst, 6, 316-323.

19079268

D.A.Traoré, A.El Ghazouani, L.Jacquamet, F.Borel, J.L.Ferrer, D.Lascoux, J.L.Ravanat, M.Jaquinod, G.Blondin, C.Caux-Thang, V.Duarte, and J.M.Latour (2009).
Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein.

Nat Chem Biol, 5, 53-59.

PDB code:

2rgv

19508286

D.P.Giedroc (2009).
Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator.

Mol Microbiol, 73, 1-4.

19221587

K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.

PLoS ONE, 4, e4473.

19114510

L.Herve-Jimenez, I.Guillouard, E.Guedon, S.Boudebbouze, P.Hols, V.Monnet, E.Maguin, and F.Rul (2009).
Postgenomic analysis of streptococcus thermophilus cocultivated in milk with Lactobacillus delbrueckii subsp. bulgaricus: involvement of nitrogen, purine, and iron metabolism.

Appl Environ Microbiol, 75, 2062-2073.

19508285

L.Jacquamet, D.A.Traoré, J.L.Ferrer, O.Proux, D.Testemale, J.L.Hazemann, E.Nazarenko, A.El Ghazouani, C.Caux-Thang, V.Duarte, and J.M.Latour (2009).
Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding.

Mol Microbiol, 73, 20-31.

PDB code:

3f8n

19400801

M.A.Sheikh, and G.L.Taylor (2009).
Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co-ordination.

Mol Microbiol, 72, 1208-1220.

PDB code:

2w57

19388025

O.Sénèque, E.Bonnet, F.L.Joumas, and J.M.Latour (2009).
Cooperative metal binding and helical folding in model peptides of treble-clef zinc fingers.

Chemistry, 15, 4798-4810.

19575568

P.Zuber (2009).
Management of oxidative stress in Bacillus.

Annu Rev Microbiol, 63, 575-597.

18831042

R.Ahmad, B.O.Brandsdal, I.Michaud-Soret, and N.P.Willassen (2009).
Ferric uptake regulator protein: binding free energy calculations and per-residue free energy decomposition.

Proteins, 75, 373-386.

19336416

Y.J.An, B.E.Ahn, A.R.Han, H.M.Kim, K.M.Chung, J.H.Shin, Y.B.Cho, J.H.Roe, and S.S.Cha (2009).
Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition.

Nucleic Acids Res, 37, 3442-3451.

PDB code:

3eyy

19788177

Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.

Chem Rev, 109, 4644-4681.

19169435

D.Lucarelli, M.L.Vasil, W.Meyer-Klaucke, and E.Pohl (2008).
The Metal-Dependent Regulators FurA and FurB from Mycobacterium Tuberculosis.

Int J Mol Sci, 9, 1548-1560.

18552126

H.Havukainen, S.Haataja, A.Kauko, A.T.Pulliainen, A.Salminen, T.Haikarainen, J.Finne, and A.C.Papageorgiou (2008).
Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.

Protein Sci, 17, 1513-1521.

PDB codes:

2ux1 2v15

18259067

Y.J.An, B.E.Ahn, J.H.Roe, and S.S.Cha (2008).
Crystallization and preliminary X-ray crystallographic analyses of Nur, a nickel-responsive transcription regulator from Streptomyces coelicolor.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 130-132.

17637984

D.P.Giedroc, and A.I.Arunkumar (2007).
Metal sensor proteins: nature's metalloregulated allosteric switches.

Dalton Trans, (), 3107-3120.

17216355

J.W.Lee, and J.D.Helmann (2007).
Functional specialization within the Fur family of metalloregulators.

Biometals, 20, 485-499.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.