PDBsum entry 5kfb

Replication, transferase/DNA

PDB id: 5kfb

Contents

Protein chain

430 a.a.

DNA/RNA

Ligands

GOL ×2

DTP

Metals

_MN ×2

_CA

Waters ×440

PDB id:

5kfb

Name:

Replication, transferase/DNA

Title:

Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 90s

Structure:

DNA polymerase eta. Chain: a. Synonym: rad30 homolog a,xeroderma pigmentosum variant type protein. Engineered: yes. DNA (5'-d( Cp Ap Tp Tp Ap Tp Gp Ap Cp Gp Cp T)-3'). Chain: t. Engineered: yes. DNA (5'-d( Ap Gp Cp Gp Tp Cp Ap T)-3'). Chain: p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polh, rad30, rad30a, xpv. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.55Å R-factor: 0.177 R-free: 0.206

Authors:

Y.Gao,W.Yang

Key ref:

Y.Gao and W.Yang (2016). Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Science, 352, 1334-1337. PubMed id: 27284197 DOI: 10.1126/science.aad9633

Date:

12-Jun-16 Release date: 22-Jun-16

Protein chain

Q9Y253  (POLH_HUMAN) -  DNA polymerase eta from Homo sapiens

Seq: 713 a.a.

Struc: 430 a.a.

DNA/RNA chains

C-A-T-T-A-T-G-A-C-G-C-T 12 bases

A-G-C-G-T-C-A-T 8 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1126/science.aad9633

Science 352:1334-1337 (2016)

PubMed id: 27284197

Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.

Y.Gao, W.Yang.

ABSTRACT

It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.