PDBsum entry 1dpr

Transcription regulation

PDB id

1dpr

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Contents

			Protein chains

					134 a.a. *

* Residue conservation analysis

PDB id:

1dpr

Links

Name:

Transcription regulation

Title:

Structures of the apo-and metal ion activated forms of the diphtheria tox repressor from corynebacterium diphtheriae

Structure:

Diphtheria tox repressor. Chain: a, b. Synonym: dtxr. Engineered: yes

Source:

Corynebacterium diphtheriae. Organism_taxid: 1717. Strain: c7(-). Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å

R-factor:

0.241

R-free:

0.417

Authors:

N.Schiering,X.Tao,J.Murphy,G.A.Petsko,D.Ringe

Key ref:

N.Schiering et al. (1995). Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae. Proc Natl Acad Sci U S A, 92, 9843-9850. PubMed id: 7568230 DOI: 10.1073/pnas.92.21.9843

Date:

06-Feb-95

Release date:

15-Sep-95

PROCHECK

	Headers

	References

Protein chains

P0DJL7 (DTXR_CORDI) - Diphtheria toxin repressor from Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)

Seq: Struc:					226 a.a. 134 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

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

DOI no: 10.1073/pnas.92.21.9843	Proc Natl Acad Sci U S A 92:9843-9850 (1995)
PubMed id: 7568230

Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.
N.Schiering, X.Tao, H.Zeng, J.R.Murphy, G.A.Petsko, D.Ringe.

ABSTRACT

The diphtheria tox repressor (DtxR) of Corynebacterium diphtheriae plays a critical role in the regulation of diphtheria toxin expression and the control of other iron-sensitive genes. The crystal structures of apo-DtxR and of the metal ion-activated form of the repressor have been solved and used to identify motifs involved in DNA and metal ion binding. Residues involved in binding of the activated repressor to the diphtheria tox operator, glutamine 43, arginine 47, and arginine 50, were located and confirmed by site-directed mutagenesis. Previous biochemical and genetic data can be explained in terms of these structures. Conformational differences between apo- and Ni-DtxR are discussed with regard to the mechanism of action of this repressor.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18761626

P.J.Brett, M.N.Burtnick, J.C.Fenno, and F.C.Gherardini (2008).
Treponema denticola TroR is a manganese- and iron-dependent transcriptional repressor.

Mol Microbiol, 70, 396-409.

17118401

M.A.DeWitt, J.I.Kliegman, J.D.Helmann, R.G.Brennan, D.L.Farrens, and A.Glasfeld (2007).
The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state.

J Mol Biol, 365, 1257-1265.

PDB codes:

2hyf 2hyg

17976643

N.Bhattacharya, M.Yi, H.X.Zhou, and T.M.Logan (2007).
Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR.

J Mol Biol, 374, 977-992.

16585757

D.M.Oram, A.D.Jacobson, and R.K.Holmes (2006).
Transcription of the contiguous sigB, dtxR, and galE genes in Corynebacterium diphtheriae: evidence for multiple transcripts and regulation by environmental factors.

J Bacteriol, 188, 2959-2973.

15667993

D.M.Oram, L.M.Must, J.K.Spinler, E.M.Twiddy, and R.K.Holmes (2005).
Analysis of truncated variants of the iron dependent transcriptional regulators from Corynebacterium diphtheriae and Mycobacterium tuberculosis.

FEMS Microbiol Lett, 243, 1-8.

15670153

F.J.Flores, C.Barreiro, J.J.Coque, and J.F.Martín (2005).
Functional analysis of two divalent metal-dependent regulatory genes dmdR1 and dmdR2 in Streptomyces coelicolor and proteome changes in deletion mutants.

FEBS J, 272, 725-735.

16352732

J.A.D'Aquino, J.Tetenbaum-Novatt, A.White, F.Berkovitch, and D.Ringe (2005).
Mechanism of metal ion activation of the diphtheria toxin repressor DtxR.

Proc Natl Acad Sci U S A, 102, 18408-18413.

PDB code:

1xcv

15487950

C.Wandersman, and P.Delepelaire (2004).
Bacterial iron sources: from siderophores to hemophores.

Annu Rev Microbiol, 58, 611-647.

15039307

D.M.Oram, A.Avdalovic, and R.K.Holmes (2004).
Analysis of genes that encode DtxR-like transcriptional regulators in pathogenic and saprophytic corynebacterial species.

Infect Immun, 72, 1885-1895.

14983039

J.F.Love, J.C.vanderSpek, V.Marin, L.Guerrero, T.M.Logan, and J.R.Murphy (2004).
Genetic and biophysical studies of diphtheria toxin repressor (DtxR) and the hyperactive mutant DtxR(E175K) support a multistep model of activation.

Proc Natl Acad Sci U S A, 101, 2506-2511.

12581348

E.Pohl, J.C.Haller, A.Mijovilovich, W.Meyer-Klaucke, E.Garman, and M.L.Vasil (2003).
Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator.

Mol Microbiol, 47, 903-915.

PDB code:

1mzb

12622807

G.M.Rodriguez, and I.Smith (2003).
Mechanisms of iron regulation in mycobacteria: role in physiology and virulence.

Mol Microbiol, 47, 1485-1494.

12837782

J.A.D'Aquino, and D.Ringe (2003).
Determinants of the SRC homology domain 3-like fold.

J Bacteriol, 185, 4081-4086.

PDB code:

1p92

12644496

J.F.Love, J.C.VanderSpek, and J.R.Murphy (2003).
The src homology 3-like domain of the diphtheria toxin repressor (DtxR) modulates repressor activation through interaction with the ancillary metal ion-binding site.

J Bacteriol, 185, 2251-2258.

12655054

M.M.Spiering, D.Ringe, J.R.Murphy, and M.A.Marletta (2003).
Metal stoichiometry and functional studies of the diphtheria toxin repressor.

Proc Natl Acad Sci U S A, 100, 3808-3813.

14580210

S.A.Lieser, T.C.Davis, J.D.Helmann, and S.M.Cohen (2003).
DNA-binding and oligomerization studies of the manganese(II) metalloregulatory protein MntR from Bacillus subtilis.

Biochemistry, 42, 12634-12642.

12270831

D.M.Oram, A.Avdalovic, and R.K.Holmes (2002).
Construction and characterization of transposon insertion mutations in Corynebacterium diphtheriae that affect expression of the diphtheria toxin repressor (DtxR).

J Bacteriol, 184, 5723-5732.

11320302

E.Pohl, J.Goranson-Siekierke, M.K.Choi, T.Roosild, R.K.Holmes, and W.G.Hol (2001).
Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity.

Acta Crystallogr D Biol Crystallogr, 57, 619-627.

PDB codes:

1fwz 1g3s 1g3t 1g3w 1g3y

11353844

L.H.Weaver, K.Kwon, D.Beckett, and B.W.Matthews (2001).
Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator.

Proc Natl Acad Sci U S A, 98, 6045-6050.

PDB code:

1hxd

11572979

P.D.Twigg, G.Parthasarathy, L.Guerrero, T.M.Logan, and D.L.Caspar (2001).
Disordered to ordered folding in the regulation of diphtheria toxin repressor activity.

Proc Natl Acad Sci U S A, 98, 11259-11264.

11004391

C.A.Boland, and W.G.Meijer (2000).
The iron dependent regulatory protein IdeR (DtxR) of Rhodococcus equi.

FEMS Microbiol Lett, 191, 1-5.

10629190

J.H.Lee, and R.K.Holmes (2000).
Characterization of specific nucleotide substitutions in DtxR-specific operators of Corynebacterium diphtheriae that dramatically affect DtxR binding, operator function, and promoter strength.

J Bacteriol, 182, 432-438.

10760146

Q.Que, and J.D.Helmann (2000).
Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins.

Mol Microbiol, 35, 1454-1468.

10657208

R.K.Holmes (2000).
Biology and molecular epidemiology of diphtheria toxin and the tox gene.

J Infect Dis, 181, S156-S167.

10339551

G.Wang, G.P.Wylie, P.D.Twigg, D.L.Caspar, J.R.Murphy, and T.M.Logan (1999).
Solution structure and peptide binding studies of the C-terminal src homology 3-like domain of the diphtheria toxin repressor protein.

Proc Natl Acad Sci U S A, 96, 6119-6124.

PDB code:

1bym

10085021

J.Goranson-Siekierke, E.Pohl, W.G.Hol, and R.K.Holmes (1999).
Anion-coordinating residues at binding site 1 are essential for the biological activity of the diphtheria toxin repressor.

Infect Immun, 67, 1806-1811.

10348851

O.Dussurget, J.Timm, M.Gomez, B.Gold, S.Yu, S.Z.Sabol, R.K.Holmes, W.R.Jacobs, and I.Smith (1999).
Transcriptional control of the iron-responsive fxbA gene by the mycobacterial regulator IdeR.

J Bacteriol, 181, 3402-3408.

9562558

J.Furui, K.Uegaki, T.Yamazaki, M.Shirakawa, M.B.Swindells, H.Harada, T.Taniguchi, and Y.Kyogoku (1998).
Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family.

Structure, 6, 491-500.

PDB codes:

1irf 1irg

9565750

J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.

Fold Des, 3, R29-R40.

9844002

L.Sun, J.vanderSpek, and J.R.Murphy (1998).
Isolation and characterization of iron-independent positive dominant mutants of the diphtheria toxin repressor DtxR.

Proc Natl Acad Sci U S A, 95, 14985-14990.

9144784

E.Pohl, X.Qui, L.M.Must, R.K.Holmes, and W.G.Hol (1997).
Comparison of high-resolution structures of the diphtheria toxin repressor in complex with cobalt and zinc at the cation-anion binding site.

Protein Sci, 6, 1114-1118.

9032054

M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.

Curr Opin Struct Biol, 7, 76-85.

9334747

M.Sunnerhagen, M.Nilges, G.Otting, and J.Carey (1997).
Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA.

Nat Struct Biol, 4, 819-826.

PDB code:

1aoy

8599765

X.Ding, H.Zeng, N.Schiering, D.Ringe, and J.R.Murphy (1996).
Identification of the primary metal ion-activation sites of the diphtheria tox repressor by X-ray crystallography and site-directed mutational analysis.

Nat Struct Biol, 3, 382-387.

PDB code:

1tdx

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 codes are shown on the right.