5KFQ

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 10 mM Mn2+ for 600s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Gao, Y.Yang, W.

(2016) Science 352: 1334-1337

  • DOI: 10.1126/science.aad9633
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. wei.yang@nih.gov.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 0 
Gene Names: POLH (RAD30, RAD30A, XPV)
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Go to Gene View: POLH
Go to UniProtKB:  Q9Y253
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')T12Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*(AS))-3')P9Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
STP
Query on STP

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)
C10 H16 N5 O11 P3 S
CCPIKNHZOWQALM-XZPDCLKESA-N
 Ligand Interaction
DPO
Query on DPO

Download SDF File 
Download CCD File 
A
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AS
Query on AS
P
DNA LINKINGC10 H14 N5 O5 P SDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.620α = 90.00
b = 98.620β = 90.00
c = 81.840γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-12 
  • Released Date: 2016-06-29 
  • Deposition Author(s): Gao, Y., Yang, W.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesIntramural DK036146-08

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations