PDBsum entry 2f52

DNA binding protein/transcription

PDB id

2f52

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Contents

			Protein chain

					67 a.a. *

* Residue conservation analysis

PDB id:

2f52

Links
- PDBe
- RCSB
- MMDB
- JenaLib
- Proteopedia
- CATH
- SCOP
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- ProSAT

Name:

DNA binding protein/transcription

Title:

Solution structure of cold shock protein cspb from bacillus subtilis in complex with heptathymidine

Structure:

Cold shock protein cspb. Chain: a. Synonym: major cold shock protein. Engineered: yes

Source:

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

NMR struc:

18 models

Authors:

M.Zeeb,H.Sticht,J.Balbach

Key ref:

M.Zeeb et al. (2006). Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution. Nucleic Acids Res, 34, 4561-4571. PubMed id: 16956971

Date:

25-Nov-05

Release date:

19-Sep-06

PROCHECK

	Headers

	References

Protein chain

P32081 (CSPB_BACSU) - Cold shock protein CspB from Bacillus subtilis (strain 168)

Seq: Struc:					67 a.a. 67 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

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

	Nucleic Acids Res 34:4561-4571 (2006)
PubMed id: 16956971

Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.
M.Zeeb, K.E.Max, U.Weininger, C.Löw, H.Sticht, J.Balbach.

ABSTRACT

Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding proteins with OB-fold. CSP are believed to function as 'RNA chaperones' and during anti-termination. We determined the solution structure of Bs-CspB bound to the single-stranded DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. Bs-CspB reveals an almost invariant conformation when bound to dT7 with only minor reorientations in loop beta1-beta2 and beta3-beta4 and of few aromatic side chains involved in base stacking. Binding studies of protein variants and mutated ssDNA demonstrated that Bs-CspB associates with ssDNA at almost diffusion controlled rates and low sequence specificity consistent with its biological function. A variation of the ssDNA affinity is accomplished solely by changes of the dissociation rate. 15N NMR relaxation and H/D exchange experiments revealed that binding of dT7 increases the stability of Bs-CspB and reduces the sub-nanosecond dynamics of the entire protein and especially of loop beta3-beta4.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21124848

A.Buttstedt, R.Winter, M.Sackewitz, G.Hause, F.X.Schmid, and E.Schwarz (2010).
Influence of the stability of a fused protein and its distance to the amyloidogenic segment on fibril formation.

PLoS One, 5, e15436.

19564956

K.M.Guardino, S.R.Sheftic, R.E.Slattery, and A.T.Alexandrescu (2009).
Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily.

Int J Mol Sci, 10, 2412-2430.

18250086

A.M.Eldridge, and D.S.Wuttke (2008).
Probing the mechanism of recognition of ssDNA by the Cdc13-DBD.

Nucleic Acids Res, 36, 1624-1633.

18391418

J.Ren, J.E.Nettleship, S.Sainsbury, N.J.Saunders, and R.J.Owens (2008).
Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 247-251.

PDB code:

3cam

18424511

M.Sackewitz, S.von Einem, G.Hause, M.Wunderlich, F.X.Schmid, and E.Schwarz (2008).
A folded and functional protein domain in an amyloid-like fibril.

Protein Sci, 17, 1044-1054.

17603075

B.L.Kormos, Y.Benitex, A.M.Baranger, and D.L.Beveridge (2007).
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model.

J Mol Biol, 371, 1405-1419.

17488853

H.P.Morgan, P.Estibeiro, M.A.Wear, K.E.Max, U.Heinemann, L.Cubeddu, M.P.Gallagher, P.J.Sadler, and M.D.Walkinshaw (2007).
Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.

Nucleic Acids Res, 35, e75.

17266726

K.E.Max, M.Zeeb, R.Bienert, J.Balbach, and U.Heinemann (2007).
Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.

FEBS J, 274, 1265-1279.

PDB code:

2hax

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.