PDBsum entry 2mre

Replication/signaling protein

PDB id: 2mre

Contents

Protein chains

79 a.a.

33 a.a.

Metals

_ZN

PDB id:

2mre

Name:

Replication/signaling protein

Title:

Nmr structure of the rad18-ubz/ubiquitin complex

Structure:

Polyubiquitin-c. Chain: a. Fragment: unp residues 1-76. Engineered: yes. E3 ubiquitin-protein ligase rad18. Chain: b. Fragment: unp residues 198-227. Synonym: postreplication repair protein rad18, hhr18, hrad18, ring finger protein 73.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubc. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: rad18, rnf73.

NMR struc:

20 models

Authors:

A.A.Rizzo,P.E.Salerno,I.Bezsonova,D.M.Korzhnev

Key ref:

A.A.Rizzo et al. (2014). NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response. Biochemistry, 53, 5895-5906. PubMed id: 25162118 DOI: 10.1021/bi500823h

Date:

03-Jul-14 Release date: 22-Oct-14

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 79 a.a.

Protein chain

Q9NS91  (RAD18_HUMAN) -  E3 ubiquitin-protein ligase RAD18 from Homo sapiens

Seq: 495 a.a.

Struc: 33 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chain A: E.C.?
• Enzyme class 2: Chain B: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[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.

DOI no: 10.1021/bi500823h

Biochemistry 53:5895-5906 (2014)

PubMed id: 25162118

NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response.

A.A.Rizzo, P.E.Salerno, I.Bezsonova, D.M.Korzhnev.

ABSTRACT

Ubiquitin-mediated interactions are critical for the cellular DNA damage response (DDR). Therefore, many DDR-related proteins contain ubiquitin-binding domains, including ubiquitin-binding zinc fingers (UBZs). The majority of these UBZ domains belong to the C2H2 (type 3 Polη-like) or C2HC (type 4 Rad18-like) family. We have used nuclear magnetic resonance (NMR) spectroscopy to characterize the binding to ubiquitin and determine the structure of the type 4 UBZ domain (UBZ4) from human Rad18, which is a key ubiquitin ligase in the DNA damage tolerance pathway responsible for monoubiquitination of the DNA sliding clamp PCNA. The Rad18-UBZ domain binds ubiquitin with micromolar affinity and adopts a β1-β2-α fold similar to the previously characterized type 3 UBZ domain (UBZ3) from the translesion synthesis DNA polymerase Polη. However, despite nearly identical structures, a disparity in the location of binding-induced NMR chemical shift perturbations shows that the Rad18-UBZ4 and Polη-UBZ3 domains bind ubiquitin in distinctly different modes. The Rad18-UBZ4 domain interacts with ubiquitin with the α-helix and strand β1 as shown by the structure of the Rad18-UBZ domain-ubiquitin complex determined in this work, while the Polη-UBZ3 domain exclusively utilizes the α-helix. Our findings suggest the existence of two classes of UBZ domains in DDR-related proteins with similar structures but unique ubiquitin binding properties and provide context for further study to establish the differential roles of these domains in the complex cellular response to DNA damage.