PDBsum entry 4f5r

Transferase, lyase/DNA

PDB id: 4f5r

Contents

Protein chain

325 a.a.

DNA/RNA

Ligands

6CF ×2

Metals

_MN ×4

_NA ×4

Waters ×414

PDB id:

4f5r

Name:

Transferase, lyase/DNA

Title:

Open and closed ternary complex of r283k DNA polymerase beta with a dctp analog in the same asymmetric unit

Structure:

DNA polymerase beta. Chain: a, b. Engineered: yes. Mutation: yes. DNA (5'-d(p Gp Tp Cp Gp G)-3'). Chain: d, c. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3'). Chain: p, g.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.20Å R-factor: 0.212 R-free: 0.278

Authors:

B.D.Freudenthal,W.A.Beard,S.H.Wilson

Key ref:

B.D.Freudenthal et al. (2012). Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure, 20, 1829-1837. PubMed id: 22959623

Date:

13-May-12 Release date: 12-Dec-12

Protein chains

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 325 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-T-C-G-G 5 bases

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

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

G-T-C-G-G 5 bases

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

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

Structure 20:1829-1837 (2012)

PubMed id: 22959623

Structures of dNTP intermediate states during DNA polymerase active site assembly.

B.D.Freudenthal, W.A.Beard, S.H.Wilson.

ABSTRACT

DNA polymerase and substrate conformational changes are essential for high-fidelity DNA synthesis. Structures of DNA polymerase (pol) β in complex with DNA show the enzyme in an "open" conformation. Subsequent to binding the nucleotide, the polymerase "closes" around the nascent base pair with two metals positioned for chemistry. However, structures of substrate/active site intermediates prior to closure are lacking. By destabilizing the closed complex, we determined unique ternary complex structures of pol β with correct and incorrect incoming nucleotides bound to the open conformation. These structures reveal that Watson-Crick hydrogen bonding is assessed upon initial complex formation. Importantly, nucleotide-bound states representing intermediate metal coordination states occur with active site assembly. The correct, but not incorrect, nucleotide maintains Watson-Crick hydrogen bonds during interconversion of these states. These structures indicate that the triphosphate of the incoming nucleotide undergoes rearrangement prior to closure, providing an opportunity to deter misinsertion and increase fidelity.