4YFU

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Closing Mechanism of DNA Polymerase I at Atomic Resolution.

Miller, B.R.Beese, L.S.Parish, C.A.Wu, E.Y.

(2015) Structure 23: 1609-1620

  • DOI: 10.1016/j.str.2015.06.016

  • PubMed Abstract: 
  • DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conf ...

    DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3'-hydroxyl.


    Organizational Affiliation

    Department of Biology, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA; Department of Chemistry, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A, D
580Geobacillus stearothermophilusMutation(s): 2 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 2
MoleculeChainsLengthOrganism
Primer DNAB,E9synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Template DNAC,F14synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TTP
Query on TTP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
2DT
Query on 2DT

Download SDF File 
Download CCD File 
B, E
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE
C10 H15 N2 O7 P
WVNRRNJFRREKAR-JGVFFNPUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
2DT
Query on 2DT
B, E
DNA LINKINGC10 H15 N2 O7 PDT
CME
Query on CME
A, D
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.230α = 90.00
b = 108.100β = 90.00
c = 151.340γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACphasing
REFMACrefinement
Cootmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-25 
  • Released Date: 2015-07-22 
  • Deposition Author(s): Wu, E.Y.

Funding OrganizationLocationGrant Number
Jeffress TrustUnited States--

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Refinement description
  • Version 1.2: 2015-09-16
    Type: Database references