PDBsum entry: 1aab

DNA-binding

PDB id: 1aab

Contents

Protein chain

83 a.a. *

* Residue conservation analysis

PDB id:

1aab

Name:

DNA-binding

Title:

Nmr structure of rat hmg1 hmga fragment

Structure:

High mobility group protein. Chain: a. Fragment: fragment a (residues 1 - 83). Synonym: hmga DNA-binding hmg-box domain a of rat hmg1. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Strain: sprague-dawley. Tissue: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

33 models

Authors:

C.H.Hardman,R.W.Broadhurst,A.R.C.Raine,K.D.Grasser, J.O.Thomas,E.D.Laue

Key ref:

C.H.Hardman et al. (1995). Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry, 34, 16596-16607. PubMed id: 8527432 DOI: 10.1021/bi00051a007

Date:

28-Oct-95 Release date: 08-Mar-96

Protein chain

P63159  (HMGB1_RAT) -  High mobility group protein B1

Seq: 215 a.a.

Struc: 83 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1021/bi00051a007

Biochemistry 34:16596-16607 (1995)

PubMed id: 8527432

Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy.

C.H.Hardman, R.W.Broadhurst, A.R.Raine, K.D.Grasser, J.O.Thomas, E.D.Laue.

ABSTRACT

HMG1 has two homologous, folded DNA-binding domains ("HMG boxes"), A and B, linked by a short basic region to an acidic C-terminal domain. Like the whole protein, which may perform an architectural role in chromatin, the individual boxes bind to DNA without sequence specificity, have a preference for distorted or prebent DNA, and are able to bend DNA and constrain negative superhelical turns. They show qualitatively similar properties with quantitative differences. We have previously determined the structure of the HMG box from the central B-domain (77 residues) by two-dimensional NMR spectroscopy, which showed that it contains a novel fold [Weir et al. (1993) EMBO J. 12, 1311-1319]. We have now determined the structure of the A-domain (as a Cys-->Ser mutant at position 22 to avoid oxidation, without effect on its DNA-binding properties or structure) using heteronuclear three- and four-dimensional NMR spectroscopy. The A-domain has a very similar global fold to the B-domain and the Drosophila protein HMG-D [Jones et al. (1994) Structure 2, 609-627]. There are small differences between A and B, in particular in the orientation of helix I, where the B-domain is more similar to HMG-D than it is to the A-domain; these differences may turn out to be related to the subtle differences in functional properties between the two domains [Teo et al. (1995) Eur. J. Biochem. 230, 943-950] and will be the subject of further investigation. NMR studies of the interaction of the A-domain of HMG1 with a short double-stranded oligonucleotide support the notion that the protein binds via the concave face of the L-shaped structure; extensive contacts with the DNA are made by the N-terminal extended strand, the N-terminus of helix I, and the C-terminus of helix II. These contacts are very similar to those seen in the LEF-1 and SRY-DNA complexes [Love et al. (1995) Nature 376, 791-795; Werner et al. (1995) Cell 81, 705-714].