PDBsum entry: 1j46

Transcription/DNA

PDB id: 1j46

Contents

Protein chain

85 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1j46

Name:

Transcription/DNA

Title:

3d solution nmr structure of the wild type hmg-box domain of the human male sex determining factor sry complexed to DNA

Structure:

Sex-determining region y protein. Chain: a. Fragment: hmg-box domain. Synonym: sry. Engineered: yes. 5'-d( Cp Cp Tp Gp Cp Ap Cp Ap Ap Ap Cp Ap Cp C)- 3'. Chain: b. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

NMR struc:

1 models

Authors:

G.M.Clore,E.C.Murphy

Key ref:

E.C.Murphy et al. (2001). Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation. J Mol Biol, 312, 481-499. PubMed id: 11563911 DOI: 10.1006/jmbi.2001.4977

Date:

23-Jul-01 Release date: 03-Oct-01

Protein chain

Q05066  (SRY_HUMAN) -  Sex-determining region Y protein

Seq: 204 a.a.

Struc: 85 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: male sex determination (1 term)
• Biochemical function: protein binding (3 terms)

DOI no: 10.1006/jmbi.2001.4977

J Mol Biol 312:481-499 (2001)

PubMed id: 11563911

Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation.

E.C.Murphy, V.B.Zhurkin, J.M.Louis, G.Cornilescu, G.M.Clore.

ABSTRACT

The HMG-box domain of the human male sex-determining factor SRY, hSRY(HMG) (comprising residues 57-140 of the full-length sequence), binds DNA sequence-specifically in the minor groove, resulting in substantial DNA bending. The majority of point mutations resulting in 46X,Y sex reversal are located within this domain. One clinical de novo mutation, M64I in the full-length hSRY sequence, which corresponds to M9I in the present hSRY(HMG) construct, acts principally by reducing the extent of DNA bending. To elucidate the structural consequences of the M9I mutation, we have solved the 3D solution structures of wild-type and M9I hSRY(HMG) complexed to a DNA 14mer by NMR, including the use of residual dipolar couplings to derive long-range orientational information. We show that the average bend angle (derived from an ensemble of 400 simulated annealing structures for each complex) is reduced by approximately 13 degrees from 54(+/-2) degrees in the wild-type complex to 41(+/-2) degrees in the M9I complex. The difference in DNA bending can be localized directly to changes in roll and tilt angles in the ApA base-pair step involved in interactions with residue 9 and partial intercalation of Ile13. The larger bend angle in the wild-type complex arises as a direct consequence of steric repulsion of the sugar of the second adenine by the bulky S(delta) atom of Met9, whose position is fixed by a hydrogen bond with the guanidino group of Arg17. In the M9I mutant, this hydrogen bond can no longer occur, and the less bulky C(gamma)m methyl group of Ile9 braces the sugar moieties of the two adenine residues, thereby decreasing the roll and tilt angles at the ApA step by approximately 8 degrees and approximately 5 degrees, respectively, and resulting in an overall difference in bend angle of approximately 13 degrees between the two complexes. To our knowledge, this is one of the first examples where the effects of a clinical mutation involving a protein-DNA complex have been visualized at the atomic level.

Selected figure(s)

Figure 8.
Figure 8. Comparison of the intermolecular contacts with DNA involving ((a), (b) and (e)) Met9 of wild-type hSRYHMG and ((c), (d) and (e)) Ile9 of the M9I mutant. In (a) and (c) the DNA is displayed as a stick represen- tation in yellow and the protein is shown as a molecular surface with the location of (a) Met9 indicated in red, (c) Ile9 in blue, and Ile13 in green (which is seen to par- tially intercalate between base-pairs 8 and 9). In (b) and (d) the DNA is displayed as a molecular surface, the protein backbone is shown as a yellow tube, and the side-chain atoms (as CPK models) of (b) Met9 are shown in red, (d) Ile9 in blue, and Ile13 in green. In (e) a stereoview of a superposition of the wild-type and M9I structures, best-fit to the base of A8 and illustrating a detailed view of the interactions of Met9 and Ile9 with the sugar moieties of A8 and A9, is shown with the wild-type in red and the mutant in blue (darker shades are used for the protein, lighter ones for the DNA). Pro- tons are shown only for the methyl groups of Met9 and Ile9 and the H20/H200 protons of A8. The S d atom of Met9 in the wild-type complex is in van der Waals con- tact with the sugar moiety of A9: the distances from the S d atom to the O-4 , C-4 and C-50 atoms of A9 are 4.2, 3.5 and 3.7 Å , respectively. The distances from the C g atom of Met9 in the wild-type to the C-20 atom of A8, and the O-4 , C-40 and C-50 atoms of A9 are 4.9, 4.5, 4.2 and 3.8 Å , respectively; the corresponding distances involving the C g m methyl group of Ile9 in the M9I mutant are 4.0, 4.3, 4.3 and 3.9 A Ê , respectively. Labels for the DNA are in italics.

Figure 10.
Figure 10. Comparison of the wild-type hSRYHMG-DNA structure with the NMR structure of the LEF-1-DNA com- plex ((a) and (b)) and the crystal structure of the HMGD-DNA complex ((c) and (d)). The hSRYHMG complex is shown in red, and the other two complexes in blue. The residue numbering employed for LEF-1 has been changed to correspond to that of the present hSRY HMG construct; to obtain the original numbering of LEF-1, subtract 3 from the indicated residue numbers. Overall views are shown in (a) and (c), and more detailed views including relevant side- chains are shown in (b) and (d). Labels for the DNA are in italics. The coordinates of the LEF-1-DNA and HMGD- DNA complexes are taken from Love et al. 13 (PDB code 2LEF) and Murphy et al. 14 (PDB code 1QRV).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 312, 481-499) copyright 2001.

Figures were selected by the author.