PDBsum entry 2c6b

Ligase

PDB id

2c6b

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Contents

			Protein chain

					46 a.a. *

			Metals

					_ZN

* Residue conservation analysis

PDB id:

2c6b

Links
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Name:

Ligase

Title:

Solution structure of the c4 zinc-finger domain of hdm2

Structure:

Ubiquitin-protein ligase e3 mdm2. Chain: a. Synonym: human mdm2, p53-binding protein mdm2, oncoprotein mdm2, double minute 2 protein, hdm2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: c41.

NMR struc:

20 models

Authors:

G.W.Yu,M.D.Allen,A.Andreeva,A.R.Fersht,M.Bycroft

Key ref:

G.W.Yu et al. (2006). Solution structure of the C4 zinc finger domain of HDM2. Protein Sci, 15, 384-389. PubMed id: 16385008 DOI: 10.1110/ps.051927306

Date:

08-Nov-05

Release date:

04-Jan-06

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:					491 a.a. 46 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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: 10.1110/ps.051927306	Protein Sci 15:384-389 (2006)
PubMed id: 16385008

Solution structure of the C4 zinc finger domain of HDM2.
G.W.Yu, M.D.Allen, A.Andreeva, A.R.Fersht, M.Bycroft.

ABSTRACT

HDM2 is a ubiquitin E3 ligase that is a key negative regulator of the tumor suppressor p53. Here, we report the determination of the solution structure of the C4 zinc finger domain of HDM2 using multidimensional NMR. The HDM2 C4 zinc finger domain has a fold consisting of a 3(10) helix followed by four beta-strands, which shares significant structural similarity to the zinc ribbon protein family. Family based sequence analysis identified two putative binding sites, one of which resembles an RNA binding motif.

Selected figure(s)



	Figure 1. NMR structures of the cis and trans forms of the HDM2 C4 zinc finger domain. An overlay of the backbone atoms of the 20 lowest energy NMR structures for the (A) trans and (B) cis forms of the HDM2 C4 zinc finger. (C) A ribbon representation of the trans (blue) and cis (red) conformers superimposed over the folded region, prepared using the program MOLSCRIPT (Kraulis 1991).		Figure 3. Comparison of zinc knuckles of HDM2 and Isoleucyl-tRNA synthetase. (A) MDM2; (B) Isoleucyl-tRNA synthetase (1ffy:A) boundto tRNA. Conserved Trp, Arg, and Cys are shown as sticks. The figure was produced using Pymol (DeLanoScientific).

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21134643

E.Escobar-Cabrera, D.K.Lau, S.Giovinazzi, A.M.Ishov, and L.P.McIntosh (2010).
Structural characterization of the DAXX N-terminal helical bundle domain and its complex with Rassf1C.

Structure, 18, 1642-1653.

PDB codes:

2kzs 2kzu

20856878

L.Jelsbak, H.Ingmer, L.Valihrach, M.T.Cohn, M.H.Christiansen, B.H.Kallipolitis, and D.Frees (2010).
The chaperone ClpX stimulates expression of Staphylococcus aureus protein A by Rot dependent and independent pathways.

PLoS One, 5, e12752.

19568783

E.G.Worrall, B.Wawrzynow, L.Worrall, M.Walkinshaw, K.L.Ball, and T.R.Hupp (2009).
Regulation of the E3 ubiquitin ligase activity of MDM2 by an N-terminal pseudo-substrate motif.

J Chem Biol, 2, 113-129.

19304800

F.E.Loughlin, R.E.Mansfield, P.M.Vaz, A.P.McGrath, S.Setiyaputra, R.Gamsjaeger, E.S.Chen, B.J.Morris, J.M.Guss, and J.P.Mackay (2009).
The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.

Proc Natl Acad Sci U S A, 106, 5581-5586.

PDB code:

3g9y

19505478

J.R.Partridge, and T.U.Schwartz (2009).
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain.

J Mol Biol, 391, 375-389.

PDB codes:

3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8

19878869

Y.Zhang, and H.Lu (2009).
Signaling to p53: ribosomal proteins find their way.

Cancer Cell, 16, 369-377.

18755053

A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.

Q Rev Biophys, 41, 41.

18713742

E.Bitto, C.A.Bingman, L.Bittova, D.A.Kondrashov, R.M.Bannen, B.G.Fox, J.L.Markley, and G.N.Phillips (2008).
Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain.

J Biol Chem, 283, 30184-30192.

PDB code:

3bvo

18611384

N.Schrader, C.Koerner, K.Koessmeier, J.A.Bangert, A.Wittinghofer, R.Stoll, and I.R.Vetter (2008).
The crystal structure of the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex.

Structure, 16, 1116-1125.

PDB codes:

2k0c 3ch5

18809412

S.G.Sivakolundu, A.Nourse, S.Moshiach, B.Bothner, C.Ashley, J.Satumba, J.Lahti, and R.W.Kriwacki (2008).
Intrinsically unstructured domains of Arf and Hdm2 form bimolecular oligomeric structures in vitro and in vivo.

J Mol Biol, 384, 240-254.

17116689

M.S.Lindström, A.Jin, C.Deisenroth, G.White Wolf, and Y.Zhang (2007).
Cancer-associated mutations in the MDM2 zinc finger domain disrupt ribosomal protein interaction and attenuate MDM2-induced p53 degradation.

Mol Cell Biol, 27, 1056-1068.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.