PDBsum entry: 1hma

DNA-binding

PDB id: 1hma

Contents

Protein chain

73 a.a. *

* Residue conservation analysis

PDB id:

1hma

Name:

DNA-binding

Title:

The solution structure and dynamics of the DNA binding domain of hmg-d from drosophila melanogaster

Structure:

Hmg-d. Chain: a. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227

NMR struc:

20 models

Authors:

D.N.M.Jones,M.A.Searles,G.L.Shaw,M.E.A.Churchill,S.S.Ner, J.Keeler,A.A.Travers,D.Neuhaus

Key ref:

D.N.Jones et al. (1994). The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster. Structure, 2, 609-627. PubMed id: 7922039 DOI: 10.1016/S0969-2126(00)00063-0

Date:

12-May-94 Release date: 31-Jul-94

Protein chain

Q05783  (HMGD_DROME) -  High mobility group protein D

Seq: 112 a.a.

Struc: 73 a.a.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1016/S0969-2126(00)00063-0

Structure 2:609-627 (1994)

PubMed id: 7922039

The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster.

D.N.Jones, M.A.Searles, G.L.Shaw, M.E.Churchill, S.S.Ner, J.Keeler, A.A.Travers, D.Neuhaus.

ABSTRACT

BACKGROUND: The HMG-box is a conserved DNA-binding motif that has been identified in many high mobility group (HMG) proteins. HMG-D is a non-histone chromosomal protein from Drosophila melanogaster that is closely related to the mammalian HMG-box proteins HMG-1 and HMG-2. Previous structures determined for an HMG-box domain from rat and hamster exhibit the same global topology, but differ significantly in detail. It has been suggested that these differences may arise from hinge motions which allow the protein to adapt to the shape of its target DNA. RESULTS: We present the solution structure of HMG-D determined by NMR spectroscopy to an overall precision of 0.85 A root mean squared deviation (rmsd) for the backbone atoms. The protein consists of an extended amino-terminal region and three alpha-helices that fold into a characteristic 'L' shape. The central core region of the molecule is highly stable and maintains an angle of approximately 80 degrees between the axes of helices 2 and 3. The backbone dynamics determined from 15N NMR relaxation measurements show a high correlation with the mean residue rmsd determined from the calculated structures. CONCLUSIONS: The structure determined for the HMG-box motif from HMG-D is essentially identical to the structure determined for the B-domain of mammalian HMG-1. Since these proteins have significantly different sequences our results indicate that the global fold and the mode of interaction with DNA are also likely to be conserved in all eukaryotes.

Selected figure(s)

Figure 1.
Figure 1. Comparison of the sequences of HMG-box motifs from HMG-D and mammalian HMG-1 and HMG-2. Residues that are conserved in all sequences shown are highlighted in red. Additional residues which are conserved between HMG-D and the B-domain of HMG-1 are highlighted in green. The sequences are numbered according to the encoded HMG-D protein. Figure 1. Comparison of the sequences of HMG-box motifs from HMG-D and mammalian HMG-1 and HMG-2. Residues that are conserved in all sequences shown are highlighted in red. Additional residues which are conserved between HMG-D and the B-domain of HMG-1 are highlighted in green. The sequences are numbered according to the encoded HMG-D protein.

Figure 10.
Figure 10. Comparison of the HMG-box domain from HMG-D (red) and the B-domain of rat HMG-1 (yellow) [12]. The structures are superimposed on the backbone N, Cα and C′ atoms corresponding to residues 12–27, 34–44 and 50–59 of HMG-D. Figure 10. Comparison of the HMG-box domain from HMG-D (red) and the B-domain of rat HMG-1 (yellow) [[3]12]. The structures are superimposed on the backbone N, Cα and C′ atoms corresponding to residues 12–27, 34–44 and 50–59 of HMG-D.

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 609-627) copyright 1994.

Figures were selected by an automated process.