4IR1

Polymerase-DNA Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Literature

A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.

Sharma, A., Kottur, J., Narayanan, N., Nair, D.T.

(2013) Nucleic Acids Res 41: 5104-5114

  • DOI: 10.1093/nar/gkt146
  • Primary Citation of Related Structures:  
    4IR1, 4IR9, 4IRC, 4IRD, 4IRK

  • PubMed Abstract: 

    • The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA presenting the four possible template nucleotides that are paired with the corresponding incoming nucleotide triphosphates ...

    The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA presenting the four possible template nucleotides that are paired with the corresponding incoming nucleotide triphosphates. In all four structures, the Ser42 residue in the active site forms interactions with the base moieties of the incipient Watson-Crick base pair. This residue is located close to the centre of the nascent base pair towards the minor groove. In vitro and in vivo assays show that the fidelity of the PolIV enzyme increases drastically when this Ser residue was mutated to Ala. In addition, the structure of PolIV with the mismatch A:C in the active site shows that the Ser42 residue plays an important role in stabilizing dCTP in a conformation compatible with catalysis. Overall, the structural, biochemical and functional data presented here show that the Ser42 residue is present at a strategic location to stabilize mismatches in the PolIV active site, and thus facilitate the appearance of transition and transversion mutations.

    Organizational Affiliation: 

    National Centre for Biological Sciences (NCBS-TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, India.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVB [auth A],
A [auth F]		352Escherichia coli K-12Mutation(s): 0 
Gene Names: b0231, dinB, dinP, JW0221
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47155
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')E [auth B],
C [auth G]		18N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')D [auth H]14N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')F [auth C]17N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FZ
Query on 1FZ
Download Ideal Coordinates CCD File 
G [auth F],
J [auth A]		5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
C10 H18 N3 O13 P3
YRKUYVYMPXAOAT-XLPZGREQSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth F],
I [auth F],
K [auth A],
L [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.75α = 90
b = 57.25β = 90.44
c = 111.301γ = 90
Software Package:
Software NamePurpose
RSQdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-01-14 
  • Released Date: 2013-04-10 
    • Deposition Author(s): Sharma, A., Nair, D.T.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Derived calculations
  • Version 1.2: 2013-05-29
    Changes: Database references