PDBsum entry 3ogu

Transferase/DNA

PDB id: 3ogu

Contents

Protein chain

326 a.a. *

DNA/RNA

Ligands

GOL

MES

Metals

_NA ×3

Waters ×335

* Residue conservation analysis

PDB id:

3ogu

Name:

Transferase/DNA

Title:

DNA polymerase beta mutant 5p20 complexed with 6bp of DNA

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. 5'-d( Cp Ap Tp Cp Tp G)-3'. Chain: t. Engineered: yes. 5'-d(p Cp Ap Gp Ap Tp G)-3'. Chain: p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic oligonucleotide. Other_details: synthetic oligonucleotide

Resolution:

1.85Å R-factor: 0.199 R-free: 0.233

Authors:

A.Marx,K.Diederichs,K.Bergen

Key ref:

S.Gieseking et al. (2011). Human DNA polymerase beta mutations allowing efficient abasic site bypass. J Biol Chem, 286, 4011-4020. PubMed id: 21107011

Date:

17-Aug-10 Release date: 24-Nov-10

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.*

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

DNA/RNA chains

C-A-T-C-T-G 6 bases

C-A-G-A-T-G 6 bases

Enzyme reactions

• Enzyme class 1: 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: E.C.4.2.99.- - ?????
• Enzyme class 3: 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

J Biol Chem 286:4011-4020 (2011)

PubMed id: 21107011

Human DNA polymerase beta mutations allowing efficient abasic site bypass.

S.Gieseking, K.Bergen, F.Di Pasquale, K.Diederichs, W.Welte, A.Marx.

ABSTRACT

No abstract given.