PDBsum entry: 1j5n

DNA binding protein/DNA

PDB-id: 1j5n

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PROCHECK

Protein chain

93 a.a. *

DNA/RNA

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1j5n

Name:

DNA binding protein/DNA

Title:

Solution structure of the non-sequence-specific hmgb protein nhp6a in complex with sry DNA

Structure:

Nonhistone chromosomal protein 6a. Chain: a. Synonym: nhp6a. Engineered: yes. 5'- d( Gp Gp Gp Gp Tp Gp Ap Tp Tp Gp Tp Tp Cp Ap G)-3'. Chain: b. Engineered: yes. Other_details: sry_dna g-rich strand.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: unlabeled DNA made on a commercial synthesizer, 15n,13c-labeled DNA made enzymatically in vitro with taq polymerase.

UniProt:

P11632 (NHP6A_YEAST)

Seq:

93 a.a.

Struc:

93 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

not givenÅ

NMR structure:

20 models

Authors:

J.E.Masse,B.Wong,Y.-M.Yen,F.H.-T.Allain,R.C.Johnson,J.Feigon

Key ref:

J.E.Masse et al. (2002). The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding.. J Mol Biol, 323, 263-284. [PubMed id: 12381320] [DOI: 10.1016/S0022-2836(02)00938-5]

Date:

15-May-02

Release date:

16-Oct-02

Related entries:

1cg7
free nhp6a protein structure

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Clefts

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Key reference

DOI no: 10.1016/S0022-2836(02)00938-5

J Mol Biol 323:263-284 (2002)

PubMed id: 12381320

The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding.

J.E.Masse, B.Wong, Y.M.Yen, F.H.Allain, R.C.Johnson, J.Feigon.

ABSTRACT

NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces cerevisiae which belongs to the HMGB protein family. Previously, we have solved the structure of NHP6A in the absence of DNA and modeled its interaction with DNA. Here, we present the refined solution structures of the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and bound forms of the protein adopt the typical L-shaped HMGB domain fold. The DNA in the complex undergoes significant structural rearrangement from its free form while the protein shows smaller but significant conformational changes in the complex. Structural and mutational analysis as well as comparison of the complex with the free DNA provides insight into the factors that contribute to binding site selection and DNA deformations in the complex. Further insight into the amino acid determinants of DNA binding by HMGB domain proteins is given by a correlation study of NHP6A and 32 other HMGB domains belonging to both the DNA-sequence-specific and non-sequence-specific families of HMGB proteins. The resulting correlations can be rationalized by comparison of solved structures of HMGB proteins.

Selected figure(s)

Figure 3.
Figure 3. (a) Stereo view of the L25, M29, Y28 wedge inserted into the T9-G10/A22-C21 step of the DNA^sry. Residues Ser26 and Asp77, which contribute to the conformation of the wedge are also displayed. (b) Surface representation of NHP6A bound to DNA^sry. Phe48, Tyr28, Met29, and Arg23 are rendered in cpk with the two aromatics shown in magenta, Met29 in pink, and Arg23 in green. DNA residues are colored blue (Gua), red (Ade), cyan (Cyt), and orange (Thy). (c) Sequence of DNA^sry shown in similar orientation as in Figure (b). Positioning of Phe48, Tyr28, Met29, and Arg23 is shown with Phe48 represented as a magenta hexagon, Tyr28 as a magenta rectangle, Met29 as a pink rectangle, and Arg23 as a green oval.

Figure 4.
Figure 4. (a) View of the NHP6A-DNA complex showing a cpk rendering (and schematic, inset) of the hydrophobic "zipper" holding helix 3 and the extended strand region together. Helix 3 is red and the extended strand is green. (b) View of the NHP6A-DNA complex showing the interaction of the N-terminal tail beginning with Lys8 with the major groove of the DNA. The DNA is shown as a surface with the negatively charged phosphate oxygen atoms in red. The core HMGB fold of the protein is shown as three cylinders and the N-terminal tail beginning with Lys8 is shown as an aqua ribbon with the positively charged side-chains shown as blue sticks.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 323, 263-284) copyright 2002.

Figures were selected by the author.