PDBsum entry 3lqc

DNA binding protein

PDB id: 3lqc

Contents

Protein chains

151 a.a. *

194 a.a. *

Ligands

CO3

Metals

_NA

Waters ×234

* Residue conservation analysis

PDB id:

3lqc

Name:

DNA binding protein

Title:

X-ray crystal structure of oxidized xrcc1 bound to DNA pol beta palm thumb domain

Structure:

DNA repair protein xrcc1. Chain: a. Synonym: x-ray repair cross-complementing protein 1. Engineered: yes. DNA polymerase beta. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: homo sapiens. Gene: xrcc1. Expressed in: escherichia coli. Expression_system_taxid: 562. Rattus norvegicus. Rat.

Resolution:

2.35Å R-factor: 0.192 R-free: 0.250

Authors:

M.J.Cuneo,J.M.Krahn,R.E.London

Key ref:

M.J.Cuneo and R.E.London (2010). Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity. Proc Natl Acad Sci U S A, 107, 6805-6810. PubMed id: 20351257

Date:

09-Feb-10 Release date: 28-Apr-10

Protein chain

P18887  (XRCC1_HUMAN) -  DNA repair protein XRCC1 from Homo sapiens

Seq: 633 a.a.

Struc: 151 a.a.

Protein chain

P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus

Seq: 335 a.a.

Struc: 194 a.a.

Enzyme reactions

• Enzyme class 1: Chain B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: Chain B: E.C.4.2.99.- - ?????
• Enzyme class 3: Chain B: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

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

Added reference

Proc Natl Acad Sci U S A 107:6805-6810 (2010)

PubMed id: 20351257

Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.

M.J.Cuneo, R.E.London.

ABSTRACT

Formation of a complex between the XRCC1 N-terminal domain (NTD) and DNA polymerase beta (Pol beta) is central to base excision repair of damaged DNA. Two crystal forms of XRCC1-NTD complexed with Pol beta have been solved, revealing that the XRCC1-NTD is able to adopt a redox-dependent alternate fold, characterized by a disulfide bond, and substantial variations of secondary structure, folding topology, and electrostatic surface. Although most of these structural changes occur distal to the interface, the oxidized XRCC1-NTD forms additional interactions with Pol beta, enhancing affinity by an order of magnitude. Transient disulfide bond formation is increasingly recognized as an important molecular regulatory mechanism. The results presented here suggest a paradigm in DNA repair in which the redox state of a scaffolding protein plays an active role in organizing the repair complex.