PDBsum entry 4ii2

Ligase

PDB id: 4ii2

Contents

Protein chains

977 a.a.

80 a.a.

149 a.a.

Ligands

ATP

PG0

EDO ×7

SO4 ×4

Metals

_MG ×2

Waters ×568

PDB id:

4ii2

Name:

Ligase

Title:

Crystal structure of ubiquitin activating enzyme 1 (uba1) in complex with the ub e2 ubc4, ubiquitin, and atp/mg

Structure:

Ubiquitin-activating enzyme e1 1. Chain: a. Fragment: uba1, unp residues 13-1012. Synonym: poly(a)+ RNA transport protein 3. Engineered: yes. Ubiquitin-60s ribosomal protein l40. Chain: b. Fragment: unp residues 1-76. Engineered: yes.

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 284812. Strain: 972 / atcc 24843. Gene: ptr3, spbc1604.21c, spbc211.09, ubiquitin activating enzyme 1 (uba1). Expressed in: escherichia coli. Expression_system_taxid: 562. Strain: strain 972 / atcc 24843.

Resolution:

2.20Å R-factor: 0.214 R-free: 0.254

Authors:

S.K.Olsen,C.D.Lima

Key ref:

S.K.Olsen and C.D.Lima (2013). Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. Mol Cell, 49, 884-896. PubMed id: 23416107 DOI: 10.1016/j.molcel.2013.01.013

Date:

19-Dec-12 Release date: 13-Feb-13

Protein chain

O94609  (UBA1_SCHPO) -  Ubiquitin-activating enzyme E1 1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 1012 a.a.

Struc: 977 a.a.

Protein chain

P0CH07  (RL402_SCHPO) -  Ubiquitin-ribosomal protein eL40B fusion protein from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 128 a.a.

Struc: 80 a.a.*

Protein chain

P46595  (UBC4_SCHPO) -  Ubiquitin-conjugating enzyme E2 4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 147 a.a.

Struc: 149 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.6.2.1.45 - E1 ubiquitin-activating enzyme.
• Reaction: ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine

• Enzyme class 3: Chain C: 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

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.

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

reference

DOI no: 10.1016/j.molcel.2013.01.013

Mol Cell 49:884-896 (2013)

PubMed id: 23416107

Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.

S.K.Olsen, C.D.Lima.

ABSTRACT

Ubiquitin (Ub) conjugation is initiated by an E1 enzyme that catalyzes carboxy-terminal Ub adenylation, thioester bond formation to a catalytic cysteine in the E1 Cys domain, and thioester transfer to a catalytic cysteine in E2 conjugating enzymes. How the E1 and E2 active sites come together during thioester transfer and how Ub E1 interacts with diverse Ub E2s remains unclear. Here we present a crystal structure of a Ub E1-E2(Ubc4)/Ub/ATP⋅Mg complex that was stabilized by induction of a disulfide bond between the E1 and E2 active sites. The structure reveals combinatorial recognition of the E2 by the E1 ubiquitin-fold domain (UFD) and Cys domain and mutational analysis, coupled with thioester transfer assays with E1, Ubc4, and other Ub E2s, show that both interfaces are important for thioester transfer. Comparison to a Ub E1/Ub/ATP⋅Mg structure reveals conformational changes in the E1 that bring the E1 and E2 active sites together.