PDBsum entry 4kld

Transferase, lyase/DNA

PDB id: 4kld

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

DCP

Metals

_CL ×4

_CA ×2

_NA ×2

Waters ×197

PDB id:

4kld

Name:

Transferase, lyase/DNA

Title:

DNA polymerase beta matched substrate complex with ca2+, 0 s

Structure:

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

Source:

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

Resolution:

1.92Å R-factor: 0.202 R-free: 0.251

Authors:

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

Key ref:

B.D.Freudenthal et al. (2013). Observing a DNA polymerase choose right from wrong. Cell, 154, 157-168. PubMed id: 23827680 DOI: 10.1016/j.cell.2013.05.048

Date:

07-May-13 Release date: 17-Jul-13

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-G-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

Added reference

DOI no: 10.1016/j.cell.2013.05.048

Cell 154:157-168 (2013)

PubMed id: 23827680

Observing a DNA polymerase choose right from wrong.

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

ABSTRACT

DNA polymerase (pol) β is a model polymerase involved in gap-filling DNA synthesis utilizing two metals to facilitate nucleotidyl transfer. Previous structural studies have trapped catalytic intermediates by utilizing substrate analogs (dideoxy-terminated primer or nonhydrolysable incoming nucleotide). To identify additional intermediates during catalysis, we now employ natural substrates (correct and incorrect nucleotides) and follow product formation in real time with 15 different crystal structures. We are able to observe molecular adjustments at the active site that hasten correct nucleotide insertion and deter incorrect insertion not appreciated previously. A third metal binding site is transiently formed during correct, but not incorrect, nucleotide insertion. Additionally, long incubations indicate that pyrophosphate more easily dissociates after incorrect, compared to correct, nucleotide insertion. This appears to be coupled to subdomain repositioning that is required for catalytic activation/deactivation. The structures provide insights into a fundamental chemical reaction that impacts polymerase fidelity and genome stability.