PDBsum entry 2is9

Transcription

PDB id

2is9

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Contents

			Protein chain

					204 a.a. *

			Ligands

					MES

			Metals

					_PT


					_CL ×4

			Waters ×168

* Residue conservation analysis

PDB id:

2is9

Links

Name:

Transcription

Title:

Structure of yeast dcn-1

Structure:

Defective in cullin neddylation protein 1. Chain: a. Fragment: residues 66-269. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dcn1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.92Å

R-factor:

0.198

R-free:

0.240

Authors:

X.Yang,J.Zhou,L.Sun,Z.Wei,J.Gao,W.Gong,R.M.Xu,Z.Rao,Y.Liu

Key ref:

X.Yang et al. (2007). Structural basis for the function of DCN-1 in protein Neddylation. J Biol Chem, 282, 24490-24494. PubMed id: 17597076 DOI: 10.1074/jbc.C700038200

Date:

16-Oct-06

Release date:

26-Jun-07

PROCHECK

	Headers

	References

Protein chain

Q12395 (DCN1_YEAST) - Defective in cullin neddylation protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					269 a.a. 204 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

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

DOI no: 10.1074/jbc.C700038200	J Biol Chem 282:24490-24494 (2007)
PubMed id: 17597076

Structural basis for the function of DCN-1 in protein Neddylation.
X.Yang, J.Zhou, L.Sun, Z.Wei, J.Gao, W.Gong, R.M.Xu, Z.Rao, Y.Liu.

ABSTRACT

Covalent modification by Nedd8 (neddylation) stimulates the ubiquitin-protein isopeptide ligase (E3) activities of Cullins. DCN-1, an evolutionarily conserved protein, promotes neddylation of Cullins in vivo, binds directly to Nedd8, and associates with Cdc53 in the budding yeast Saccharomyces cerevisiae. The 1.9A resolution structure of yeast DCN-1 shows that the region encompassing residues 66-269 has a rectangular parallelepiped-like all alpha-helical structures, consisting of an EF-hand motif N-terminal domain and a closely juxtaposed C-terminal domain with six alpha-helices. The EF-hand motif structure is highly similar to that of the c-Cbl ubiquitin E3 ligase. We also demonstrate that DCN-1 directly binds to Rbx-1, a factor important for protein neddylation. The structural and biochemical results are consistent with the role of DCN-1 as a scaffold protein in a multisubunit neddylation E3 ligase complex.

Selected figure(s)



	Figure 2. Structure of DCN-1.A, a stereo ribbon diagram showing the overall structure of DCN-1. The structure is colored from the N to the C termini with blue to red. B, a surface representation of the DCN-1 structure. B1 (side 1) and B3 (side 2) show the distribution of conserved residues on the two sides of the protein surface. Absolutely conserved residues are indicated in blue, and highly conserved residues are shown in green, using the convention defined in the legend for Fig. 1. The arrow points to the position of Glu-260, which is colored in red. Electrostatic potential on the protein surface is shown in B2 and B4, which are oriented the same as in B1 and B3, respectively. Positively charged regions are shown in red, negatively charged regions are in blue, and neutral ones are in white.		Figure 3. Superposition of c-Cbl and DCN-1.A, a stereo diagram of superimposed DCN-1 (blue) and c-Cbl (gray) EF-hand motifs. A red sphere represents a calcium ion bound to the c-Cbl EF-hand motif. B, superposition of c-Cbl (only EF-hand and helix bundle motifs are shown) with DCN-1 to show the different spatial arrangement of the two helix bundle motifs.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21288713

D.M.Duda, D.C.Scott, M.F.Calabrese, E.S.Zimmerman, N.Zheng, and B.A.Schulman (2011).
Structural regulation of cullin-RING ubiquitin ligase complexes.

Curr Opin Struct Biol, 21, 257-264.

20832729

D.C.Scott, J.K.Monda, C.R.Grace, D.M.Duda, R.W.Kriwacki, T.Kurz, and B.A.Schulman (2010).
A dual E3 mechanism for Rub1 ligation to Cdc53.

Mol Cell, 39, 784-796.

PDB codes:

3o2p 3o2u 3o6b

21103004

D.Wei, and Y.Sun (2010).
Small RING finger proteins RBX1 and RBX2 of SCF E3 ubiquitin ligases: the role in cancer and as cancer targets.

Genes Cancer, 1, 700-707.

19114460

J.Gilkerson, J.Hu, J.Brown, A.Jones, T.P.Sun, and J.Callis (2009).
Isolation and characterization of cul1-7, a recessive allele of CULLIN1 that disrupts SCF function at the C terminus of CUL1 in Arabidopsis thaliana.

Genetics, 181, 945-963.

19617556

N.Meyer-Schaller, Y.C.Chou, I.Sumara, D.D.Martin, T.Kurz, N.Katheder, K.Hofmann, L.G.Berthiaume, F.Sicheri, and M.Peter (2009).
The human Dcn1-like protein DCNL3 promotes Cul3 neddylation at membranes.

Proc Natl Acad Sci U S A, 106, 12365-12370.

19286981

W.Jonkers, and M.Rep (2009).
Lessons from fungal F-box proteins.

Eukaryot Cell, 8, 677-695.

18826954

A.Y.Kim, C.C.Bommeljé, B.E.Lee, Y.Yonekawa, L.Choi, L.G.Morris, G.Huang, A.Kaufman, R.J.Ryan, B.Hao, Y.Ramanathan, and B.Singh (2008).
SCCRO (DCUN1D1) is an essential component of the E3 complex for neddylation.

J Biol Chem, 283, 33211-33220.

18282298

D.R.Bosu, and E.T.Kipreos (2008).
Cullin-RING ubiquitin ligases: global regulation and activation cycles.

Cell Div, 3, 7.

18802447

G.Rabut, and M.Peter (2008).
Function and regulation of protein neddylation. 'Protein modifications: beyond the usual suspects' review series.

EMBO Rep, 9, 969-976.

18444905

S.K.Hotton, and J.Callis (2008).
Regulation of cullin RING ligases.

Annu Rev Plant Biol, 59, 467-489.

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.