PDBsum entry 4r62

Nuclear protein

PDB id: 4r62

Contents

Protein chains

149 a.a.

78 a.a.

Ligands

ACT

Waters ×12

PDB id:

4r62

Name:

Nuclear protein

Title:

Structure of rad6~ub

Structure:

Ubiquitin-conjugating enzyme e2 2. Chain: a. Fragment: rad6. Synonym: radiation sensitivity protein 6, ubiquitin carrier protein ubc2, ubiquitin-protein ligase ubc2. Engineered: yes. Mutation: yes. Ubiquitin-40s ribosomal protein s27a. Chain: b.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: rad6, ubc2, ygl058w. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human.

Resolution:

2.28Å R-factor: 0.213 R-free: 0.265

Authors:

P.Kumar,C.Wolberger

Key ref:

P.Kumar et al. (2015). Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity. Nucleic Acids Res, 43, 9039-9050. PubMed id: 26286193 DOI: 10.1093/nar/gkv845

Date:

22-Aug-14 Release date: 02-Sep-15

Protein chain

P06104  (UBC2_YEAST) -  Ubiquitin-conjugating enzyme E2 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 172 a.a.

Struc: 149 a.a.*

Protein chain

P62979  (RS27A_HUMAN) -  Ubiquitin-ribosomal protein eS31 fusion protein from Homo sapiens

Seq: 156 a.a.

Struc: 78 a.a.

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

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: 10.1093/nar/gkv845

Nucleic Acids Res 43:9039-9050 (2015)

PubMed id: 26286193

Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity.

P.Kumar, P.Magala, K.R.Geiger-Schuller, A.Majumdar, J.R.Tolman, C.Wolberger.

ABSTRACT

Rad6 is a yeast E2 ubiquitin conjugating enzyme that monoubiquitinates histone H2B in conjunction with the E3, Bre1, but can non-specifically modify histones on its own. We determined the crystal structure of a Rad6∼Ub thioester mimic, which revealed a network of interactions in the crystal in which the ubiquitin in one conjugate contacts Rad6 in another. The region of Rad6 contacted is located on the distal face of Rad6 opposite the active site, but differs from the canonical E2 backside that mediates free ubiquitin binding and polyubiquitination activity in other E2 enzymes. We find that free ubiquitin interacts weakly with both non-canonical and canonical backside residues of Rad6 and that mutations of non-canonical residues have deleterious effects on Rad6 activity comparable to those observed to mutations in the canonical E2 backside. The effect of non-canonical backside mutations is similar in the presence and absence of Bre1, indicating that contacts with non-canonical backside residues govern the intrinsic activity of Rad6. Our findings shed light on the determinants of intrinsic Rad6 activity and reveal new ways in which contacts with an E2 backside can regulate ubiquitin conjugating activity.