PDBsum entry: 1j7d

Unknown function

PDB id: 1j7d

Contents

Protein chains

140 a.a. *

149 a.a. *

Waters ×190

* Residue conservation analysis

PDB id:

1j7d

Name:

Unknown function

Title:

Crystal structure of hmms2-hubc13

Structure:

Mms2. Chain: a. Engineered: yes. Ubiquitin-conjugating enzyme e2-17 kda. Chain: b. Synonym: ubc13. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.85Å R-factor: 0.215 R-free: 0.244

Authors:

T.F.Moraes,R.A.Edwards,S.Mckenna,L.Pashushok,W.Xiao, J.N.M.Glover,M.J.Ellison

Key ref:

T.F.Moraes et al. (2001). Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13. Nat Struct Biol, 8, 669-673. PubMed id: 11473255 DOI: 10.1038/90373

Date:

16-May-01 Release date: 08-Aug-01

Protein chain

Q15819  (UB2V2_HUMAN) -  Ubiquitin-conjugating enzyme E2 variant 2

Seq: 145 a.a.

Struc: 140 a.a.

Protein chain

P61088  (UBE2N_HUMAN) -  Ubiquitin-conjugating enzyme E2 N

Seq: 152 a.a.

Struc: 149 a.a.

Enzyme reactions

• Enzyme class: Chain B: E.C.6.3.2.19 - Ubiquitin--protein ligase.
• Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: UBC13-UEV1A complex (6 terms)
• Biological process: cell proliferation (30 terms)
• Biochemical function: protein binding (7 terms)

reference

DOI no: 10.1038/90373

Nat Struct Biol 8:669-673 (2001)

PubMed id: 11473255

Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13.

T.F.Moraes, R.A.Edwards, S.McKenna, L.Pastushok, W.Xiao, J.N.Glover, M.J.Ellison.

ABSTRACT

The ubiquitin conjugating enzyme complex Mms2-Ubc13 plays a key role in post-replicative DNA repair in yeast and the NF-kappaB signal transduction pathway in humans. This complex assembles novel polyubiquitin chains onto yet uncharacterized protein targets. Here we report the crystal structure of a complex between hMms2 (Uev1) and hUbc13 at 1.85 A resolution and a structure of free hMms2 at 1.9 A resolution. These structures reveal that the hMms2 monomer undergoes a localized conformational change upon interaction with hUbc13. The nature of the interface provides a physical basis for the preference of Mms2 for Ubc13 as a partner over a variety of other structurally similar ubiquitin-conjugating enzymes. The structure of the hMms2-hUbc13 complex provides the conceptual foundation for understanding the mechanism of Lys 63 multiubiquitin chain assembly and for its interactions with the RING finger proteins Rad5 and Traf6.

Selected figure(s)

Figure 2.
Figure 2. The interface created by the hMms2 -hUbc13 complex. a, The interface of hMms2 and hUbc13 (hMms2 in yellow and hUbc13 in blue) with an 90° clockwise rotation with respect to Fig. 1. Residues in the interface are labeled (hMms2 in yellow and hUbc13 in blue). The active site Cys in hUbc13 is labeled in black. b, Sequence alignments of the interface residues in hUbc13 and hMms2 with homologs/orthologs in humans and yeast. Residues in the hMms2 -hUbc13 interface are colored in yellow and blue, respectively, and residues in the proposed hUbc13 -E3(RING) interface are colored in green. Residues in the E2 that interact with ubiquitin are colored in red. Absolutely and partially conserved residues between the E2 homologs are shaded in black and gray, respectively. Secondary structural elements are shown above (for the E2s) and below (for Uev) the sequence alignment. c, Stereo view of the experimental, MAD-phased complex to 2.0 Å resolution with the electron density map contoured at 1.2 . The electron density is superimposed on the refined model.

Figure 4.
Figure 4. Molecular surface of hMms2 -hUbc13 heterodimer. The molecular surface of the hMms2 and hUbc13 is shaded yellow and blue, respectively, in approximately the same orientation as Fig. 1a. The potential ubiquitin binding site and E3 RING finger-binding residues are colored in red and green, respectively, as in Fig. 2b. The hUbc13 active site Cys residue is colored yellow. Arrows indicate the clefts on either side of the heterodimer interface where the noncovalent ubiquitin may be positioned. The figure was drawn using the programs Molscript27 and GRASP28.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 669-673) copyright 2001.

Figures were selected by an automated process.