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PDBsum entry 1dbq
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DNA-binding regulatory protein
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PDB id
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1dbq
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Contents |
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* Residue conservation analysis
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DOI no:
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Cell
83:147-155
(1995)
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PubMed id:
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Mechanism of corepressor-mediated specific DNA binding by the purine repressor.
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M.A.Schumacher,
K.Y.Choi,
F.Lu,
H.Zalkin,
R.G.Brennan.
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ABSTRACT
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The modulation of the affinity of DNA-binding proteins by small molecule
effectors for cognate DNA sites is common to both prokaryotes and eukaryotes.
However, the mechanisms by which effector binding to one domain affects DNA
binding by a distal domain are poorly understood structurally. In initial
studies to provide insight into the mechanism of effector-modulated DNA binding
of the lactose repressor family, we determined the crystal structure of the
purine repressor bound to a corepressor and purF operator. To extend our
understanding, we have determined the structure of the corepressor-free
corepressor-binding domain of the purine repressor at 2.2 A resolution. In the
unliganded state, structural changes in the corepressor-binding pocket cause
each subunit to rotate open by as much as 23 degrees, the consequences of which
are the disengagement of the minor groove-binding hinge helices and
repressor-DNA dissociation.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.A.Schumacher,
M.Sprehe,
M.Bartholomae,
W.Hillen,
and
R.G.Brennan
(2011).
Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.
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Nucleic Acids Res,
39,
2931-2942.
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PDB codes:
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E.H.Bromley,
N.J.Kuwada,
M.J.Zuckermann,
R.Donadini,
L.Samii,
G.A.Blab,
G.J.Gemmen,
B.J.Lopez,
P.M.Curmi,
N.R.Forde,
D.N.Woolfson,
and
H.Linke
(2009).
The Tumbleweed: towards a synthetic proteinmotor.
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HFSP J,
3,
204-212.
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L.Swint-Kruse,
and
K.S.Matthews
(2009).
Allostery in the LacI/GalR family: variations on a theme.
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Curr Opin Microbiol,
12,
129-137.
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H.Zhan,
M.Taraban,
J.Trewhella,
and
L.Swint-Kruse
(2008).
Subdividing repressor function: DNA binding affinity, selectivity, and allostery can be altered by amino acid substitution of nonconserved residues in a LacI/GalR homologue.
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Biochemistry,
47,
8058-8069.
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M.Resch,
H.Striegl,
E.M.Henssler,
M.Sevvana,
C.Egerer-Sieber,
E.Schiltz,
W.Hillen,
and
Y.A.Muller
(2008).
A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR.
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Nucleic Acids Res,
36,
4390-4401.
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PDB code:
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M.Taraban,
H.Zhan,
A.E.Whitten,
D.B.Langley,
K.S.Matthews,
L.Swint-Kruse,
and
J.Trewhella
(2008).
Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein.
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J Mol Biol,
376,
466-481.
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S.Meinhardt,
and
L.Swint-Kruse
(2008).
Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives.
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Proteins,
73,
941-957.
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B.Loll,
M.Kowalczyk,
C.Alings,
A.Chieduch,
J.Bardowski,
W.Saenger,
and
J.Biesiadka
(2007).
Structure of the transcription regulator CcpA from Lactococcus lactis.
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Acta Crystallogr D Biol Crystallogr,
63,
431-436.
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PDB code:
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M.D.Daily,
and
J.J.Gray
(2007).
Local motions in a benchmark of allosteric proteins.
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Proteins,
67,
385-399.
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N.Horstmann,
G.Seidel,
L.M.Aung-Hilbrich,
and
W.Hillen
(2007).
Residues His-15 and Arg-17 of HPr participate differently in catabolite signal processing via CcpA.
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J Biol Chem,
282,
1175-1182.
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S.Tungtur,
S.M.Egan,
and
L.Swint-Kruse
(2007).
Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence.
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Proteins,
68,
375-388.
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Y.G.Gao,
M.Yao,
H.Itou,
Y.Zhou,
and
I.Tanaka
(2007).
The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: a novel homodimer assembling and the implication for effector-binding mode.
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Protein Sci,
16,
1878-1886.
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PDB codes:
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I.S.Franco,
L.J.Mota,
C.M.Soares,
and
I.de Sá-Nogueira
(2006).
Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding.
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J Bacteriol,
188,
3024-3036.
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M.A.Schumacher,
G.Seidel,
W.Hillen,
and
R.G.Brennan
(2006).
Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation.
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J Biol Chem,
281,
6793-6800.
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PDB code:
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W.Müller,
N.Horstmann,
W.Hillen,
and
H.Sticht
(2006).
The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis.
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FEBS J,
273,
1251-1261.
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M.A.Schumacher,
G.S.Allen,
M.Diel,
G.Seidel,
W.Hillen,
and
R.G.Brennan
(2004).
Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.
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Cell,
118,
731-741.
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PDB codes:
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L.Swint-Kruse,
C.Larson,
B.M.Pettitt,
and
K.S.Matthews
(2002).
Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR.
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Protein Sci,
11,
778-794.
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U.Magnusson,
B.N.Chaudhuri,
J.Ko,
C.Park,
T.A.Jones,
and
S.L.Mowbray
(2002).
Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations.
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J Biol Chem,
277,
14077-14084.
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D.M.van Aalten,
C.C.DiRusso,
and
J.Knudsen
(2001).
The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.
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EMBO J,
20,
2041-2050.
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PDB codes:
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H.Zhang,
and
A.Wang
(2001).
Functional analysis of three amino acid residues of purR repressor, Trpl47, Gln-218 and Gln-292 inSalmonella typhimurium.
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Sci China C Life Sci,
44,
184-191.
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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.
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Proc Natl Acad Sci U S A,
98,
6045-6050.
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PDB code:
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L.Swint-Kruse,
C.R.Elam,
J.W.Lin,
D.R.Wycuff,
and
K.Shive Matthews
(2001).
Plasticity of quaternary structure: twenty-two ways to form a LacI dimer.
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Protein Sci,
10,
262-276.
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C.M.Falcon,
and
K.S.Matthews
(1999).
Glycine insertion in the hinge region of lactose repressor protein alters DNA binding.
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J Biol Chem,
274,
30849-30857.
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E.E.Zheleznova,
P.N.Markham,
A.A.Neyfakh,
and
R.G.Brennan
(1999).
Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter.
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Cell,
96,
353-362.
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PDB codes:
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E.Küster-Schöck,
A.Wagner,
U.Völker,
and
W.Hillen
(1999).
Mutations in catabolite control protein CcpA showing glucose-independent regulation in Bacillus megaterium.
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J Bacteriol,
181,
7634-7638.
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S.A.Gavigan,
T.Nguyen,
N.Nguyen,
and
D.F.Senear
(1999).
Role of multiple CytR binding sites on cooperativity, competition, and induction at the Escherichia coli udp promoter.
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J Biol Chem,
274,
16010-16019.
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A.Kraus,
E.Küster,
A.Wagner,
K.Hoffmann,
and
W.Hillen
(1998).
Identification of a co-repressor binding site in catabolite control protein CcpA.
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Mol Microbiol,
30,
955-963.
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H.Xu,
M.Moraitis,
R.J.Reedstrom,
and
K.S.Matthews
(1998).
Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA.
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J Biol Chem,
273,
8958-8964.
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J.H.Kim,
M.I.Voskuil,
and
G.H.Chambliss
(1998).
NADP, corepressor for the Bacillus catabolite control protein CcpA.
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Proc Natl Acad Sci U S A,
95,
9590-9595.
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U.Hars,
R.Horlacher,
W.Boos,
W.Welte,
and
K.Diederichs
(1998).
Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose.
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Protein Sci,
7,
2511-2521.
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PDB codes:
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B.D.Nelson,
C.Manoil,
and
B.Traxler
(1997).
Insertion mutagenesis of the lac repressor and its implications for structure-function analysis.
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J Bacteriol,
179,
3721-3728.
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C.S.Barbier,
S.A.Short,
and
D.F.Senear
(1997).
Allosteric mechanism of induction of CytR-regulated gene expression. Cytr repressor-cytidine interaction.
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J Biol Chem,
272,
16962-16971.
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H.Onaka,
M.Sugiyama,
and
S.Horinouchi
(1997).
A mutation at proline-115 in the A-factor receptor protein of Streptomyces griseus abolishes DNA-binding ability but not ligand-binding ability.
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J Bacteriol,
179,
2748-2752.
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M.A.Kercher,
P.Lu,
and
M.Lewis
(1997).
Lac repressor-operator complex.
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Curr Opin Struct Biol,
7,
76-85.
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M.A.Schumacher,
A.Glasfeld,
H.Zalkin,
and
R.G.Brennan
(1997).
The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
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J Biol Chem,
272,
22648-22653.
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PDB code:
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T.Yamaoka,
M.Kondo,
S.Honda,
H.Iwahana,
M.Moritani,
S.Ii,
K.Yoshimoto,
and
M.Itakura
(1997).
Amidophosphoribosyltransferase limits the rate of cell growth-linked de novo purine biosynthesis in the presence of constant capacity of salvage purine biosynthesis.
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J Biol Chem,
272,
17719-17725.
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M.H.Saier,
and
T.M.Ramseier
(1996).
The catabolite repressor/activator (Cra) protein of enteric bacteria.
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J Bacteriol,
178,
3411-3417.
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R.T.Sauer
(1996).
Lac repressor at last.
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Structure,
4,
219-222.
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A.J.Berk
(1995).
Biochemistry meets genetics in the holoenzyme.
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Proc Natl Acad Sci U S A,
92,
11952-11954.
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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.
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Links
