PDBsum entry 1qrv

Gene regulation/DNA

PDB id: 1qrv

Contents

Protein chains

73 a.a. *

DNA/RNA

Metals

_NA

Waters ×116

* Residue conservation analysis

PDB id:

1qrv

Name:

Gene regulation/DNA

Title:

Crystal structure of the complex of hmg-d and DNA

Structure:

DNA (5'-d( Gp Cp Gp Ap Tp Ap Tp Cp Gp C)-3'). Chain: c, d. Engineered: yes. High mobility group protein d. Chain: a, b. Fragment: residues 2-74. Synonym: hmg-d. Engineered: yes

Source:

Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.238 R-free: 0.288

Authors:

F.V.Murphy Iv,R.M.Sweet,M.E.A.Churchill

Key ref:

F.V.Murphy et al. (1999). The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J, 18, 6610-6618. PubMed id: 10581235 DOI: 10.1093/emboj/18.23.6610

Date:

15-Jun-99 Release date: 18-Dec-99

Protein chains

Q05783  (HMGD_DROME) -  High mobility group protein D from Drosophila melanogaster

Seq: 112 a.a.

Struc: 73 a.a.

DNA/RNA chains

G-C-G-A-T-A-T-C-G-C 10 bases

G-C-G-A-T-A-T-C-G-C 10 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/18.23.6610

EMBO J 18:6610-6618 (1999)

PubMed id: 10581235

The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition.

F.V.Murphy, R.M.Sweet, M.E.Churchill.

ABSTRACT

The high mobility group (HMG) chromosomal proteins, which are common to all eukaryotes, bind DNA in a non-sequence-specific fashion to promote chromatin function and gene regulation. They interact directly with nucleosomes and are believed to be modulators of chromatin structure. They are also important in V(D)J recombination and in activating a number of regulators of gene expression, including p53, Hox transcription factors and steroid hormone receptors, by increasing their affinity for DNA. The X-ray crystal structure, at 2.2 A resolution, of the HMG domain of the Drosophila melanogaster protein, HMG-D, bound to DNA provides the first detailed view of a chromosomal HMG domain interacting with linear DNA and reveals the molecular basis of non-sequence-specific DNA recognition. Ser10 forms water-mediated hydrogen bonds to DNA bases, and Val32 with Thr33 partially intercalates the DNA. These two 'sequence-neutral' mechanisms of DNA binding substitute for base-specific hydrogen bonds made by equivalent residues of the sequence-specific HMG domain protein, lymphoid enhancer factor-1. The use of multiple intercalations and water-mediated DNA contacts may prove to be generally important mechanisms by which chromosomal proteins bind to DNA in the minor groove.

Selected figure(s)

Figure 1.
Figure 1 Structure of the HMG-box of HMG-D bound to DNA. (A) Sequence comparison of sequence-specific and non-sequence-specific HMG domains. The sequences are aligned and numbered according to the HMG-D structure, with helices, I, II and II depicted by black boxes (Jones et al., 1994; Baxevanis and Landsman, 1995). Residues shown from structural and modeling studies to intercalate the DNA are outlined in black (Love et al., 1995; Werner et al., 1995a,b; Balaeff et al., 1998; Allain et al., 1999; Ohndorf et al., 1999). Residues that are conserved between the two HMG-box families are shaded in gray, whereas those residues that consistently differ between the two families of HMG domains are highlighted in cyan and brown (Balaeff et al., 1998; Churchill et al., 1999). (B) Stereo view of the refined (2|F[o]| - |F[c]|) electron density map contoured at a level of 1.9 . The protein and DNA are colored using standard CPK coloring, with water molecules and a sodium ion represented by red and blue spheres, respectively. (C) Ribbon diagram in stereo view of the complex. HMG-D is depicted in cyan, the DNA in gray, and structural water molecules found in the protein and at the DNA interface in red. Several side chains that interact with the DNA, Ser10, Tyr12, Met13, Asn17, Arg20, Val32, Thr33 and Ala36, are shown in green. The protein is well ordered from residue 4 to 72, and the DNA is well ordered throughout except for base cytosine 10, which adopts two conformations in the crystal (only one conformation is shown).

Figure 3.
Figure 3 Structural features involved in non-sequence-specific DNA recognition. (A) View of HMG-D protein from this structure (cyan) superimposed on the structure of the LEF-1 -DNA complex (Love et al., 1995) (PDB accession No. 2lef; coral) in the same orientation as Figure 1C. Side chains, selected on the basis of their potential involvement in DNA specificity, are shown. Detailed view of the interaction of residue 10 from both HMG-D (B) and LEF-1 (C). HMG-D protein is in cyan, LEF-1 protein is in coral, DNA is in gray, and black dashed lines depict proposed hydrogen bonds with distances between donors and acceptors shown. The Ser10 hydroxyl oxygen of HMG-D makes water-mediated interactions with adenine 6 N3 and thymine 7 O4'. The LEF-1 Asn10 makes direct hydrogen bonds to guanine 9 N3 and thymine 8 O2 (in this LEF-1 model).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6610-6618) copyright 1999.

Figures were selected by the author.

Author's comment

DNA in chromatin is packaged and condensed into higher order structures. Through active and passive mechanisms it can be made accessible to factors involved in processes, such as transcription, DNA replication, and DNA repair, through a complex array of protein-DNA interactions, protein-protein interactions, and covalent modifications.
The chromosomal proteins that bind DNA directly and are important for the definition of chromatin structure and regulation of gene expression must be able to bind to many different DNA sequences. This is in contrast to better characterized proteins, such as transcription factors, that recognize a specific sequence of DNA. Histone H1 and the HMG-box proteins are examples of chromosomal proteins that bind to the linker DNA (between nucleosomes) and recognize distinct features of DNA structure, such as shape and flexibility. How do these proteins recognize DNA?
We have determined the structure of the complex of HMG-D bound to linear duplex DNA using X-ray crystallography (Figure 1). Through this structural analysis, we have learned how the Drosophila melanogaster HMG-box protein HMG-D binds to DNA non-sequence-specifically, and now understand many of the features of the protein that are important for protein induced DNA bending. HMG-D severely bends the DNA by binding and partially intercalating residues in the DNA minor groove. The structure of this non-sequence-specific protein-DNA complex is similar to homologous sequence-specific complexes, except for the lack of sequence-specific hydrogen bonds (Figure 3). Instead, hydrophobic interactions and water mediated non-specific hydrogen bonds stabilize the complex.
Mair Churchill