PDBsum entry 2zvl

Transferase

PDB id: 2zvl

Contents

Protein chains

(+ 0 more) 245 a.a. *

11 a.a. *

13 a.a. *

12 a.a. *

Ligands

LYS-HIS-THR-LEU-ASP-ILE-PHE-PHE-LYS-PRO

SO4 ×4

Metals

_ZN ×6

Waters ×120

* Residue conservation analysis

PDB id:

2zvl

Name:

Transferase

Title:

Crystal structure of pcna in complex with DNA polymerase kappa fragment

Structure:

Proliferating cell nuclear antigen. Chain: a, b, c, d, e, f. Synonym: pcna, cyclin. Engineered: yes. DNA polymerase kappa. Chain: u, v, w, x, y, z. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pcna. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized peptide

Resolution:

2.50Å R-factor: 0.229 R-free: 0.289

Authors:

A.Hishiki,H.Hashimoto,T.Hanafusa,K.Kamei,E.Ohashi,T.Shimizu,H.Ohmori, M.Sato

Key ref:

A.Hishiki et al. (2009). Structural Basis for Novel Interactions between Human Translesion Synthesis Polymerases and Proliferating Cell Nuclear Antigen. J Biol Chem, 284, 10552-10560. PubMed id: 19208623 DOI: 10.1074/jbc.M809745200

Date:

11-Nov-08 Release date: 10-Feb-09

Protein chains

P12004  (PCNA_HUMAN) -  Proliferating cell nuclear antigen from Homo sapiens

Seq: 261 a.a.

Struc: 245 a.a.

Protein chains

No UniProt id for this chain

Struc: 11 a.a.

Protein chains

No UniProt id for this chain

Struc: 13 a.a.

Protein chain

No UniProt id for this chain

Struc: 12 a.a.

Enzyme reactions

• Enzyme class: Chains U, Z: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1074/jbc.M809745200

J Biol Chem 284:10552-10560 (2009)

PubMed id: 19208623

Structural Basis for Novel Interactions between Human Translesion Synthesis Polymerases and Proliferating Cell Nuclear Antigen.

A.Hishiki, H.Hashimoto, T.Hanafusa, K.Kamei, E.Ohashi, T.Shimizu, H.Ohmori, M.Sato.

ABSTRACT

Translesion synthesis (TLS) is a DNA damage tolerance mechanism that allows continued DNA synthesis, even in the presence of damaged DNA templates. Mammals have multiple DNA polymerases specialized for TLS, including Poleta, Poliota, and Polkappa. These enzymes show preferential bypass for different lesions. Proliferating cell nuclear antigen (PCNA), which functions as a sliding clamp for the replicative polymerase Poldelta, also interacts with the three TLS polymerases. Although many PCNA-binding proteins have a highly conserved sequence termed the PCNA-interacting protein box (PIP-box), Poleta, Poliota, and Polkappa have a noncanonical PIP-box sequence. In response to DNA damage, Lys-164 of PCNA undergoes ubiquitination by the RAD6-RAD18 complex, and the ubiquitination is considered to facilitate TLS. Consistent with this, these three TLS polymerases have one or two ubiquitin binding domains and are recruited to replication forks via interactions with ubiquitinated PCNA involving the noncanonical PIP-box and ubiquitin binding domain. However, it is unclear how these TLS polymerases interact with PCNA. To address the structural basis for interactions between different TLS polymerases and PCNA, we determined crystal structures of PCNA bound to peptides containing the noncanonical PIP-box of these polymerases. We show that the three PIP-box peptides interact with PCNA in different ways, both from one another and from canonical PIP-box peptides. Especially, the PIP-box of Poliota adopts a novel structure. Furthermore, these structures enable us to speculate how these TLS polymerases interact with Lys-164-monoubiquitinated PCNA. Our results will provide clues to understanding the mechanism of preferential recruitment of TLS polymerases to the stalled forks.

Selected figure(s)

Figure 3.
Hydrophobic plug-socket interaction of the Polη (A) or Polι (B) peptide with PCNA and superimposition of PIP-box structures bound to PCNA (C). A and B, PCNA is shown by a surface model, and residues of PCNA that interact with the three-forked hydrophobic plug are colored gray. PIP-box residues are shown by stick models. Residues of PCNA that interact with the Met-701 (p1) residue of Polη in the Q-pocket are colored light pink. C, structures of p21, Polη, Polκ, and Polι bound to PCNA are shown in light blue, pink, green, and yellow, respectively. PIP-box residues are shown by stick models, and only some PIP-box residues of Polι are denoted.

Figure 5.
Proposed models of the interaction of Lys-164-monoubiquitinated PCNA with Polη or Polκ (A) and Polι (B). The ubiquitin moieties linked to Lys-164 are shown by ellipsoids. N- and C-terminal sides of TLS polymerase fragments are indicated by N and C, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 10552-10560) copyright 2009.

Figures were selected by an automated process.