DNA binding protein

PDB id

1i11

Contents

			Protein chain

					70 a.a. *

* Residue conservation analysis

PDB id:

1i11

Links

Name:

DNA binding protein

Title:

Solution structure of the DNA binding domain, sox-5 hmg box from mouse

Structure:

Transcription factor sox-5. Chain: a. Fragment: hmg box. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Organ: testis. Gene: sox-5. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

30 models

Authors:

P.D.Cary,C.M.Read,B.Davis,P.C.Driscoll,C.Crane-Robinson

Key ref:

P.D.Cary et al. (2001). Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5. Protein Sci, 10, 83-98. PubMed id: 11266597 DOI: 10.1110/ps.32801

Date:

30-Jan-01

Release date:

14-Feb-01

PROCHECK

	Headers

	References

Protein chain

P35710 (SOX5_MOUSE) - Transcription factor SOX-5

Seq: Struc:

Seq: Struc:					763 a.a. 70 a.a.

Key:

PfamA domain

PfamB domain

Secondary structure

CATH domain



		Gene Ontology (GO) functional annotation

Cellular component	nucleus	1 term
Biochemical function	DNA binding	1 term

DOI no: 10.1110/ps.32801	Protein Sci 10:83-98 (2001)
PubMed id: 11266597

Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5.
P.D.Cary, C.M.Read, B.Davis, P.C.Driscoll, C.Crane-Robinson.

ABSTRACT

The fold of the murine Sox-5 (mSox-5) HMG box in free solution has been determined by multidimensional NMR using (15)N-labeled protein and has been found to adopt the characteristic twisted L-shape made up of two wings: the major wing comprising helix 1 (F10--F25) and helix 2 (N32--A43), the minor wing comprising helix 3 (P51--Y67) in weak antiparallel association with the N-terminal extended segment. (15)N relaxation measurements show considerable mobility (reduced order parameter, S(2)) in the minor wing that increases toward the amino and carboxy termini of the chain. The mobility of residues C-terminal to Q62 is significantly greater than the equivalent residues of non-sequence-specific boxes, and these residues show a weaker association with the extended N-terminal segment than in non-sequence boxes. Comparison with previously determined structures of HMG boxes both in free solution and complexed with DNA shows close similarity in the packing of the hydrophobic cores and the relative disposition of the three helices. Only in hSRY/DNA does the arrangement of aromatic sidechains differ significantly from that of mSox-5, and only in rHMG1 box 1 bound to cisplatinated DNA does helix 1 have no kink. Helix 3 in mSox-5 is terminated by P68, a conserved residue in DNA sequence-specific HMG boxes, which results in the chain turning through approximately 90 degrees.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19304746

T.A.Gangelhoff, P.S.Mungalachetty, J.C.Nix, and M.E.Churchill (2009).
Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.

Nucleic Acids Res, 37, 3153-3164.

PDB code:

3fgh

19452555

Z.Liu, J.Zhang, X.Wang, Y.Ding, J.Wu, and Y.Shi (2009).
Temperature-induced partially unfolded state of hUBF HMG Box-5: conformational and dynamic investigations of the Box-5 thermal intermediate ensemble.

Proteins, 77, 432-447.

12771212

J.Klass, F.V.Murphy, S.Fouts, M.Serenil, A.Changela, J.Siple, and M.E.Churchill (2003).
The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity.

Nucleic Acids Res, 31, 2852-2864.

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.