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Transcription regulation
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PDB id
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1leb
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.88
- Repressor lexA.
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Reaction:
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Hydrolysis of Ala-|-Gly bond in repressor lexA.
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Gene Ontology (GO) functional annotation
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Biological process
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proteolysis
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1 term
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Biochemical function
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serine-type endopeptidase activity
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1 term
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Embo J
13:3936-3944
(1994)
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PubMed id:
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Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy.
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R.H.Fogh,
G.Ottleben,
H.Rüterjans,
M.Schnarr,
R.Boelens,
R.Kaptein.
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ABSTRACT
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The structure of the 84 residue DNA binding domain of the Escherichia coli LexA
repressor has been determined from NMR data using distance geometry and
restrained molecular dynamics. The assignment of the 1H NMR spectrum of the
molecule, derived from 2- and 3-D homonuclear experiments, is also reported. A
total of 613 non-redundant distance restraints were used to give a final family
of 28 structures. The structured region of the molecule consisted of residues
4-69 and yielded a r.m.s. deviation from an average of 0.9 A for backbone and
1.6 A for all heavy atoms. The structure contains three regular alpha-helices at
residues 6-21 (I), 28-35 (II) and 41-52 (III), and an antiparallel beta-sheet at
residues 56-58 and 66-68. Helices II and III form a variant helix-turn-helix DNA
binding motif, with an unusual one residue insert at residue 38. The topology of
the LexA DNA binding domain is found to be the same as for the DNA binding
domains of the catabolic activator protein, human histone 5, the HNF-3/fork head
protein and the Kluyveromyces lactis heat shock transcription factor.
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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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S.E.Battle,
F.Meyer,
J.Rello,
V.L.Kung,
and
A.R.Hauser
(2008).
Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals.
|
| |
J Bacteriol, 190,
7130-7140.
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Y.Meroz,
and
D.Horn
(2008).
Biological roles of specific peptides in enzymes.
|
| |
Proteins, 72,
606-612.
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E.S.Groban,
M.B.Johnson,
P.Banky,
P.G.Burnett,
G.L.Calderon,
E.C.Dwyer,
S.N.Fuller,
B.Gebre,
L.M.King,
I.N.Sheren,
L.D.Von Mutius,
T.M.O'Gara,
and
C.M.Lovett
(2005).
Binding of the Bacillus subtilis LexA protein to the SOS operator.
|
| |
Nucleic Acids Res, 33,
6287-6295.
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|
|
|
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J.W.Lee,
R.Kusumoto,
K.M.Doherty,
G.X.Lin,
W.Zeng,
W.H.Cheng,
C.von Kobbe,
R.M.Brosh,
J.S.Hu,
and
V.A.Bohr
(2005).
Modulation of Werner syndrome protein function by a single mutation in the conserved RecQ domain.
|
| |
J Biol Chem, 280,
39627-39636.
|
|
|
|
|
|
|
M.K.Yang,
S.R.Su,
and
V.L.Sung
(2005).
Identification and characterization of a second lexA gene of Xanthomonas axonopodis Pathovar citri.
|
| |
Appl Environ Microbiol, 71,
3589-3598.
|
|
|
|
|
|
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F.Domain,
L.Houot,
F.Chauvat,
and
C.Cassier-Chauvat
(2004).
Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation.
|
| |
Mol Microbiol, 53,
65-80.
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|
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|
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F.Kühner,
L.T.Costa,
P.M.Bisch,
S.Thalhammer,
W.M.Heckl,
and
H.E.Gaub
(2004).
LexA-DNA bond strength by single molecule force spectroscopy.
|
| |
Biophys J, 87,
2683-2690.
|
|
|
|
|
|
|
H.Fan,
and
A.E.Mark
(2004).
Refinement of homology-based protein structures by molecular dynamics simulation techniques.
|
| |
Protein Sci, 13,
211-220.
|
|
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|
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M.F.Susin,
H.R.Perez,
R.L.Baldini,
and
S.L.Gomes
(2004).
Functional and structural analysis of HrcA repressor protein from Caulobacter crescentus.
|
| |
J Bacteriol, 186,
6759-6767.
|
|
|
|
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|
|
W.A.McLaughlin,
D.W.Kulp,
J.de la Cruz,
X.J.Lu,
C.L.Lawson,
and
H.M.Berman
(2004).
A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
|
| |
J Struct Funct Genomics, 5,
255-265.
|
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|
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A.R.Fernández de Henestrosa,
J.Cuñé,
G.Mazón,
B.L.Dubbels,
D.A.Bazylinski,
and
J.Barbé
(2003).
Characterization of a new LexA binding motif in the marine magnetotactic bacterium strain MC-1.
|
| |
J Bacteriol, 185,
4471-4482.
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H.Fan,
and
A.E.Mark
(2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
|
| |
Proteins, 53,
111-120.
|
|
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|
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|
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N.Mizuno,
G.Voordouw,
K.Miki,
A.Sarai,
and
Y.Higuchi
(2003).
Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif.
|
| |
Structure, 11,
1133-1140.
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PDB code:
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A.R.Fernández de Henestrosa,
J.Cuñé,
I.Erill,
J.K.Magnuson,
and
J.Barbé
(2002).
A green nonsulfur bacterium, Dehalococcoides ethenogenes, with the LexA binding sequence found in gram-positive organisms.
|
| |
J Bacteriol, 184,
6073-6080.
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I.Narumi,
K.Satoh,
M.Kikuchi,
T.Funayama,
T.Yanagisawa,
Y.Kobayashi,
H.Watanabe,
and
K.Yamamoto
(2001).
The LexA protein from Deinococcus radiodurans is not involved in RecA induction following gamma irradiation.
|
| |
J Bacteriol, 183,
6951-6956.
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|
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K.S.Makarova,
A.A.Mironov,
and
M.S.Gelfand
(2001).
Conservation of the binding site for the arginine repressor in all bacterial lineages.
|
| |
Genome Biol, 2,
RESEARCH0013.
|
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|
|
|
|
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M.Abedi,
G.Caponigro,
J.Shen,
S.Hansen,
T.Sandrock,
and
A.Kamb
(2001).
Transcriptional transactivation by selected short random peptides attached to lexA-GFP fusion proteins.
|
| |
BMC Mol Biol, 2,
10.
|
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Y.Luo,
R.A.Pfuetzner,
S.Mosimann,
M.Paetzel,
E.A.Frey,
M.Cherney,
B.Kim,
J.W.Little,
and
N.C.Strynadka
(2001).
Crystal structure of LexA: a conformational switch for regulation of self-cleavage.
|
| |
Cell, 106,
585-594.
|
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|
PDB codes:
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E.Pérez-Rueda,
and
J.Collado-Vides
(2000).
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
|
| |
Nucleic Acids Res, 28,
1838-1847.
|
|
|
|
|
|
|
K.S.Gajiwala,
and
S.K.Burley
(2000).
Winged helix proteins.
|
| |
Curr Opin Struct Biol, 10,
110-116.
|
|
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|
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|
|
M.Okuda,
Y.Watanabe,
H.Okamura,
F.Hanaoka,
Y.Ohkuma,
and
Y.Nishimura
(2000).
Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
|
| |
EMBO J, 19,
1346-1356.
|
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|
PDB codes:
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R.J.Lewis,
S.Krzywda,
J.A.Brannigan,
J.P.Turkenburg,
K.Muchová,
E.J.Dodson,
I.Barák,
and
A.J.Wilkinson
(2000).
The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography.
|
| |
Mol Microbiol, 38,
198-212.
|
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PDB code:
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|
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R.Mohana-Borges,
A.B.Pacheco,
F.J.Sousa,
D.Foguel,
D.F.Almeida,
and
J.L.Silva
(2000).
LexA repressor forms stable dimers in solution. The role of specific dna in tightening protein-protein interactions.
|
| |
J Biol Chem, 275,
4708-4712.
|
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|
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|
|
C.M.Groft,
S.N.Uljon,
R.Wang,
and
M.H.Werner
(1998).
Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly.
|
| |
Proc Natl Acad Sci U S A, 95,
9117-9122.
|
|
|
PDB codes:
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|
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:
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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.
|
|
|
|
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|
|
P.Oertel-Buchheit,
J.Reinbolt,
M.John,
M.Granger-Schnarr,
and
M.Schnarr
(1998).
A LexA mutant repressor with a relaxed inter-domain linker.
|
| |
Protein Sci, 7,
512-515.
|
|
|
|
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|
|
A.Herbert,
J.Alfken,
Y.G.Kim,
I.S.Mian,
K.Nishikura,
and
A.Rich
(1997).
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase.
|
| |
Proc Natl Acad Sci U S A, 94,
8421-8426.
|
|
|
|
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|
|
H.Kondo,
A.Nakagawa,
J.Nishihira,
Y.Nishimura,
T.Mizuno,
and
I.Tanaka
(1997).
Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site.
|
| |
Nat Struct Biol, 4,
28-31.
|
|
|
PDB code:
|
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|
K.W.Winterling,
A.S.Levine,
R.E.Yasbin,
and
R.Woodgate
(1997).
Characterization of DinR, the Bacillus subtilis SOS repressor.
|
| |
J Bacteriol, 179,
1698-1703.
|
|
|
|
|
|
|
M.A.Kercher,
P.Lu,
and
M.Lewis
(1997).
Lac repressor-operator complex.
|
| |
Curr Opin Struct Biol, 7,
76-85.
|
|
|
|
|
|
|
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:
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W.D.Kohn,
C.T.Mant,
and
R.S.Hodges
(1997).
Alpha-helical protein assembly motifs.
|
| |
J Biol Chem, 272,
2583-2586.
|
|
|
|
|
|
|
B.Sheehan,
A.Klarsfeld,
R.Ebright,
and
P.Cossart
(1996).
A single substitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence.
|
| |
Mol Microbiol, 20,
785-797.
|
|
|
|
|
|
|
H.Goulaouic,
and
S.A.Chow
(1996).
Directed integration of viral DNA mediated by fusion proteins consisting of human immunodeficiency virus type 1 integrase and Escherichia coli LexA protein.
|
| |
J Virol, 70,
37-46.
|
|
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|
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K.S.Pai,
D.E.Bussiere,
F.Wang,
C.A.Hutchison,
S.W.White,
and
D.Bastia
(1996).
The structure and function of the replication terminator protein of Bacillus subtilis: identification of the 'winged helix' DNA-binding domain.
|
| |
EMBO J, 15,
3164-3173.
|
|
|
|
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|
|
L.W.Donaldson,
J.M.Petersen,
B.J.Graves,
and
L.P.McIntosh
(1996).
Solution structure of the ETS domain from murine Ets-1: a winged helix-turn-helix DNA binding motif.
|
| |
EMBO J, 15,
125-134.
|
|
|
PDB codes:
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S.L.Shaner,
and
E.S.Gaissarian
(1996).
Binding of Escherichia coli LexA repressor to the RecA operator.
|
| |
J Mol Recognit, 9,
468-473.
|
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D.Porte,
P.Oertel-Buchheit,
M.Granger-Schnarr,
and
M.Schnarr
(1995).
Fos leucine zipper variants with increased association capacity.
|
| |
J Biol Chem, 270,
22721-22730.
|
|
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|
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M.B.Swindells
(1995).
Identification of a common fold in the replication terminator protein suggests a possible mode for DNA binding.
|
| |
Trends Biochem Sci, 20,
300-302.
|
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R.H.Folmer,
M.Nilges,
R.N.Konings,
and
C.W.Hilbers
(1995).
Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.
|
| |
EMBO J, 14,
4132-4142.
|
|
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PDB code:
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R.M.Knegtel,
R.H.Fogh,
G.Ottleben,
H.Rüterjans,
P.Dumoulin,
M.Schnarr,
R.Boelens,
and
R.Kaptein
(1995).
A model for the LexA repressor DNA complex.
|
| |
Proteins, 21,
226-236.
|
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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
code is
shown on the right.
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Links
