PDBsum entry 4php

Transferase,lyase/DNA

PDB id: 4php

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

XG4

Metals

_MN ×2

_NA ×2

Waters ×82

PDB id:

4php

Name:

Transferase,lyase/DNA

Title:

Structure of human DNA polymerase beta complexed with t in the template base paired with incoming non-hydrolyzable gtp and manganese

Structure:

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

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: enterobacteria phage l1. Expression_system_taxid: 268588

Resolution:

2.60Å R-factor: 0.185 R-free: 0.262

Authors:

M.C.Koag,S.Lee

Key ref:

M.C.Koag and s.lee The spontaneous base substitution mechanisms of human polymerase beta. To be published, .

Date:

06-May-14 Release date: 06-May-15

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

C-C-G-A-C-T-G-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G-C 10 bases

G-T-C-G-G 5 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