PDBsum entry: 1adr

Transcription regulation

PDB-id

1adr

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Protein chain

* Residue conservation analysis

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PDB id:

1adr

Name:

Transcription regulation

Title:

Determination of the nuclear magnetic resonance structure of the DNA-binding domain of the p22 c2 repressor (1-76) in solution and comparison with the DNA-binding domain of the 434 repressor

Structure:

P22 c2 repressor. Chain: a. Engineered: yes

Source:

Enterobacteria phage p22. Organism_taxid: 10754

UniProt:

P69202 (RPC2_BPP22)

Seq:

216 a.a.

Struc:

76 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Resolution:

not givenÅ

NMR structure:

20 models

Authors:

P.Sevillasierra,G.Otting,K.Wuthrich

Key ref:

P.Sevilla-Sierra et al. (1994). Determination of the nuclear magnetic resonance structure of the DNA-binding domain of the P22 c2 repressor (1 to 76) in solution and comparison with the DNA-binding domain of the 434 repressor.. J Mol Biol, 235, 1003-1020. [PubMed id: 8289306] [DOI: 10.1006/jmbi.1994.1053]

Date:

19-Jul-93

Release date:

31-Jan-94

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Key reference

DOI no: 10.1006/jmbi.1994.1053 J Mol Biol 235:1003-1020 (1994)

PubMed id: 8289306

Determination of the nuclear magnetic resonance structure of the DNA-binding domain of the P22 c2 repressor (1 to 76) in solution and comparison with the DNA-binding domain of the 434 repressor.

P.Sevilla-Sierra, G.Otting, K.Wüthrich.

ABSTRACT

The solution structure of the N-terminal DNA-binding domain of the P22 c2 repressor (residues 1 to 76) was determined by nuclear magnetic resonance (NMR) spectroscopy. The structure determination was based on nearly complete sequence-specific resonance assignments for 1H, 13C and 15N, and tables of the chemical shifts for all three nuclei are included here. A group of 20 conformers was calculated from the NMR constraints using the program DIANA, and energy-minimized using an implementation of the AMBER force field in the program OPAL. The core of the protein formed by residues 5 to 68 is structurally well defined, with an average of 0.7 A for the root-mean-square deviations calculated for the backbone atoms of the individual conformers relative to the mean coordinates. The N-terminal tetrapeptide segment and the C-terminal octapeptide segment are flexibly disordered. The molecular architecture includes five alpha-helical segments with residues 6 to 17, 21 to 28, 32 to 39, 47 to 57 and 61 to 65. The length and relative orientation of these helices are closely similar to the arrangement of corresponding regular secondary structures in the DNA-binding domain of the 434 repressor, with the sole exception of the fourth helix, which is one turn longer at its amino-terminal end than the corresponding helix in the 434 repressor. This extension of the fourth helix implies that the DNA-binding mode of the P22 c2 repressor must be somewhat different from that observed for the 434 repressor. Exact superposition of two P22 c2 repressor DNA-binding domains for best fit of corresponding polypeptide backbone atoms onto the two 434 repressor DNA-binding domains in the crystal structure of the 434 repressor-DNA complex would result in a model of the P22 c2 repressor-DNA complex which could not accommodate the fourth helices because of steric overlap.

Literature references that cite this PDB file's key reference

PubMed id Reference

19255093 K.V.Loscha, K.Jaudzems, C.Ioannou, X.C.Su, F.R.Hill, G.Otting, N.E.Dixon, and E.Liepinsh (2009).
A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader.

Nucleic Acids Res, 37, 2395-2404.

PDB code: 2k7r

17452361 X.C.Su, S.Jergic, M.A.Keniry, N.E.Dixon, and G.Otting (2007).
Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit.

Nucleic Acids Res, 35, 2825-2832.

PDB code: 2aya

17010164 X.C.Su, P.M.Schaeffer, K.V.Loscha, P.H.Gan, N.E.Dixon, and G.Otting (2006).
Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase.

FEBS J, 273, 4997-5009.

PDB code: 2haj

12598646 K.R.LeFevre, and M.H.Cordes (2003).
Retroevolution of lambda Cro toward a stable monomer.

Proc Natl Acad Sci U S A, 100, 2345-2350.

11574466 E.Liepinsh, M.Trexler, A.Kaikkonen, J.Weigelt, L.Bányai, L.Patthy, and G.Otting (2001).
NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.

EMBO J, 20, 5347-5353.

PDB code: 1jbi

10707026 K.Steinmetzer, A.Hillisch, J.Behlke, and S.Brantl (2000).
Transcriptional repressor CopR: structure model-based localization of the deoxyribonucleic acid binding motif.

Proteins, 38, 393-406.

9521100 N.N.Alexandrov, and R.Luethy (1998).
Alignment algorithm for homology modeling and threading.

Protein Sci, 7, 254-258.

9305641 E.Liepinsh, L.L.Ilag, G.Otting, and C.F.Ibáñez (1997).
NMR structure of the death domain of the p75 neurotrophin receptor.

EMBO J, 16, 4999-5005.

PDB code: 1ngr

9153301 J.Chen, S.Pongor, and A.Simoncsits (1997).
Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs.

Nucleic Acids Res, 25, 2047-2054.

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

9242655 S.P.Hilchey, L.Wu, and G.B.Koudelka (1997).
Recognition of nonconserved bases in the P22 operator by P22 repressor requires specific interactions between repressor and conserved bases.

J Biol Chem, 272, 19898-19905.

8844842 P.Luginbühl, J.Wu, O.Zerbe, C.Ortenzi, P.Luporini, and K.Wüthrich (1996).
The NMR solution structure of the pheromone Er-11 from the ciliated protozoan Euplotes raikovi.

Protein Sci, 5, 1512-1522.

PDB code: 1ery

8563626 S.Y.Chung, and S.Subbiah (1995).
The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins.

Protein Sci, 4, 2300-2309.

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.