PDBsum entry 3a33

Ligase

PDB id

3a33

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Contents

			Protein chains

					150 a.a. *


					76 a.a. *

			Ligands

					GOL

			Waters ×62

* Residue conservation analysis

PDB id:

3a33

Links

Name:

Ligase

Title:

Ubch5b~ubiquitin conjugate

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a. Synonym: ubiquitin-protein ligase d2, ubiquitin carrier protein d2, ubiquitin-conjugating enzyme e2-17 kda 2, e2(17)kb 2. Engineered: yes. Mutation: yes. Ubiquitin. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubch5b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å

R-factor:

0.231

R-free:

0.280

Authors:

E.Sakata,T.Satoh,S.Yamamoto,Y.Yamaguchi,M.Yagi-Utsumi,E.Kurimoto, S.Wakatsuki,K.Kato

Key ref:

E.Sakata et al. (2010). Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates. Structure, 18, 138-147. PubMed id: 20152160

Date:

08-Jun-09

Release date:

24-Nov-09

PROCHECK

	Headers

	References

Protein chain

P62837 (UB2D2_HUMAN) - Ubiquitin-conjugating enzyme E2 D2 from Homo sapiens

Seq: Struc:					147 a.a. 150 a.a.*

Protein chain

P0CG48 (UBC_HUMAN) - Polyubiquitin-C from Homo sapiens

Seq: Struc:

Seq: Struc:					685 a.a. 76 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class 2:

Chain A: E.C.2.3.2.23 - E2 ubiquitin-conjugating enzyme.

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

Reaction:

S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine

Enzyme class 3:

Chain A: E.C.2.3.2.24 - (E3-independent) E2 ubiquitin-conjugating enzyme.

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

Reaction:

S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N₆- monoubiquitinyl-[acceptor protein]-L-lysine

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

	Structure 18:138-147 (2010)
PubMed id: 20152160

Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates.
E.Sakata, T.Satoh, S.Yamamoto, Y.Yamaguchi, M.Yagi-Utsumi, E.Kurimoto, K.Tanaka, S.Wakatsuki, K.Kato.

ABSTRACT

E2 ubiquitin-conjugating enzymes catalyze the attachment of ubiquitin to lysine residues of target proteins. The UbcH5b E2 enzyme has been shown to play a key role in the initiation of the ubiquitination of substrate proteins upon action of several E3 ligases. Here we have determined the 2.2 A crystal structure of an intermediate of UbcH5b~ubiquitin (Ub) conjugate, which is assembled into an infinite spiral through the backside interaction. This active complex may provide multiple E2 active sites, enabling efficient ubiquitination of substrates. Indeed, biochemical assays support a model in which the self-assembled UbcH5b~Ub can serve as a bridge for the gap between the lysine residue of the substrate and the catalytic cysteine of E2.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22842904

A.Plechanovová, E.G.Jaffray, M.H.Tatham, J.H.Naismith, and R.T.Hay (2012).
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.

Nature, 489, 115-120.

PDB code:

4ap4

22902369

H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, and D.T.Huang (2012).
BIRC7-E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer.

Nat Struct Mol Biol, 19, 876-883.

PDB code:

4auq

21857666

A.Plechanovová, E.G.Jaffray, S.A.McMahon, K.A.Johnson, I.Navrátilová, J.H.Naismith, and R.T.Hay (2011).
Mechanism of ubiquitylation by dimeric RING ligase RNF4.

Nat Struct Mol Biol, 18, 1052-1059.

PDB code:

2xeu

21474069

A.Saha, S.Lewis, G.Kleiger, B.Kuhlman, and R.J.Deshaies (2011).
Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate.

Mol Cell, 42, 75-83.

21532592

D.M.Wenzel, A.Lissounov, P.S.Brzovic, and R.E.Klevit (2011).
UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids.

Nature, 474, 105-108.

21396940

I.Bosanac, L.Phu, B.Pan, I.Zilberleyb, B.Maurer, V.M.Dixit, S.G.Hymowitz, and D.S.Kirkpatrick (2011).
Modulation of K11-linkage formation by variable loop residues within UbcH5A.

J Mol Biol, 408, 420-431.

PDB code:

3ptf

21158740

D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.

Biochem J, 433, 31-42.

21095585

I.Bosanac, I.E.Wertz, B.Pan, C.Yu, S.Kusam, C.Lam, L.Phu, Q.Phung, B.Maurer, D.Arnott, D.S.Kirkpatrick, V.M.Dixit, and S.G.Hymowitz (2010).
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.

Mol Cell, 40, 548-557.

PDB codes:

3oj3 3oj4

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 code is shown on the right.