PDBsum entry 5dfl

Ligase/signaling protein

PDB id: 5dfl

Contents

Protein chains

76 a.a.

199 a.a.

Ligands

GOL ×3

Waters ×57

PDB id:

5dfl

Name:

Ligase/signaling protein

Title:

Crystal structure of ube2k~ubiquitin conjugate

Structure:

Ubiquitin. Chain: b. Engineered: yes. Ubiquitin-conjugating enzyme e2 k. Chain: a. Synonym: huntingtin-interacting protein 2,hip-2,ubiquitin carrier protein,ubiquitin-conjugating enzyme e2-25 kda,ubiquitin-conjugating enzyme e2-25k,ubiquitin-protein ligase. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubb. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ube2k, hip2, lig. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.197 R-free: 0.235

Authors:

A.J.Middleton,C.L.Day

Key ref:

A.J.Middleton and C.L.Day (2015). The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K. Sci Rep, 5, 16793. PubMed id: 26592444 DOI: 10.1038/srep16793

Date:

27-Aug-15 Release date: 02-Dec-15

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.

Protein chain

P61086  (UBE2K_HUMAN) -  Ubiquitin-conjugating enzyme E2 K from Homo sapiens

Seq: 200 a.a.

Struc: 199 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

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

DOI no: 10.1038/srep16793

Sci Rep 5:16793 (2015)

PubMed id: 26592444

The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K.

A.J.Middleton, C.L.Day.

ABSTRACT

The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.