PDBsum entry 2hdp

Ligase

PDB id: 2hdp

Contents

Protein chains

63 a.a. *

Metals

_ZN ×4

* Residue conservation analysis

PDB id:

2hdp

Name:

Ligase

Title:

Solution structure of hdm2 ring finger domain

Structure:

Ubiquitin-protein ligase e3 mdm2. Chain: a, b. Fragment: ring finger domain. Synonym: p53-binding protein mdm2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mdm2. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

M.Kostic,T.Matt,M.Yamout-Martinez,H.J.Dyson,P.E.Wright

Key ref:

M.Kostic et al. (2006). Solution structure of the Hdm2 C2H2C4 RING, a domain critical for ubiquitination of p53. J Mol Biol, 363, 433-450. PubMed id: 16965791 DOI: 10.1016/j.jmb.2006.08.027

Date:

20-Jun-06 Release date: 21-Nov-06

Protein chains

Q00987  (MDM2_HUMAN) -  E3 ubiquitin-protein ligase Mdm2 from Homo sapiens

Seq: 491 a.a.

Struc: 63 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1016/j.jmb.2006.08.027

J Mol Biol 363:433-450 (2006)

PubMed id: 16965791

Solution structure of the Hdm2 C2H2C4 RING, a domain critical for ubiquitination of p53.

M.Kostic, T.Matt, M.A.Martinez-Yamout, H.J.Dyson, P.E.Wright.

ABSTRACT

Regulation of the transcriptional response to the tumor suppressor p53 occurs at many levels, including control of its transcriptional activity, and of its stability and concentration within the cell. p53 stability is regulated by the protein Hdm2, an E3 ubiquitin ligase that binds to p53 and promotes its ubiquitination and degradation. The C-terminal domain of Hdm2, which is critical for this activity, has been classified as a RING domain on the basis of sequence homology, although it lacks the canonical set of zinc ligands (RING domains typically have C3HC4 or C4C4 zinc coordination). Here, we report the solution structure of the C2H2C4 RING domain of Hdm2(429-491), which reveals a symmetrical dimer with a unique cross-brace zinc-binding scheme. Each subunit has one Cys4 Zn site and one His2Cys2 Zn site. The global fold of each subunit is similar to those reported for other RING domains, with a compact betabetaalphabeta fold, a small hydrophobic core, and two Zn ions, which are essential for maintaining the domain structure. The dimer structure is maintained by an extensive interface that buries a large hydrophobic area on each subunit. It has been proposed that Hdm2 and its homologue HdmX form a stable heterodimer through their RING domains, resulting in a synergistic increase in observed E3 activity. To test this proposal, we prepared an HdmX RING construct and showed by NMR titration that it forms a tight 1:1 complex with the Hdm2 RING. The resonances most perturbed by heterodimer formation are located within the subunit interface of the homodimer, far removed from the surface expected to form the docking site of the E2 ubiquitin-conjugating enzyme, providing a structure-based rationale for the function of the RING domains in p53 ubiquitination.

Selected figure(s)

Figure 6.
Figure 6. Solution structure of Hdm2(429–491) C2H2C4 RING domain. (a) Superposition of an ensemble of 20 lowest energy structures of the Hdm2(429–491) C2H2C4 RING homodimer, with the two subunits colored green and gold. The first eight and the last residue are not well-defined and are omitted for clarity. Zinc ions are shown as gray spheres. The Figure was prepared using PyMOL [http://www.pymol.sourceforge.net/]. (b) A ribbon representation of the lowest energy structure of a single subunit of Hdm2(429–491), showing the distribution of regular secondary structure elements and the location of two Zn^2+-binding sites. The side-chains of the zinc ligands are shown as balls, colored black (C), blue (N) or yellow (S). This Figure was prepared using MOLMOL.^78

Figure 10.
Figure 10. Structural overlay of the UbcH7/c-Cbl complex (PDB 1FBV)^55 with the UbcH5b structure (PDB 2ESK)^65 and the lowest-energy structure of the Hdm2(429–491) homodimer. This Figure was prepared using MOLMOL.^78

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 433-450) copyright 2006.

Figures were selected by an automated process.