4YFU

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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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: https://doi.org/10.1016/j.str.2015.06.016
  • Primary Citation of Related Structures:  
    4YFU

  • 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 conformational change that is difficult to characterize experimentally on an atomic level ...

    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 Biochemistry, Duke University Medical Center, 255 Nanaline H. Duke Building, Durham, NC 27710, USA. Electronic address: ewu@richmond.edu.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA,
B [auth D]		580Geobacillus stearothermophilusMutation(s): 2 
Gene Names: polA
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
Primer DNAC [auth B],
E		9synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
Template DNAD [auth C],
F		14synthetic construct
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP
Download Ideal Coordinates CCD File 
I [auth A]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		A,
B [auth D]		L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
G, H
sucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.23α = 90
b = 108.1β = 90
c = 151.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2015-07-22 
    • Deposition Author(s): Wu, E.Y.
Funding OrganizationLocationGrant Number
Jeffress TrustUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Refinement description
  • Version 1.2: 2015-09-16
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2022-04-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary