2IMW

Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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Literature

Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase.

Fiala, K.A., Brown, J.A., Ling, H., Kshetry, A.K., Zhang, J., Taylor, J.S., Yang, W., Suo, Z.

(2007) J Mol Biol 365: 590-602

  • DOI: 10.1016/j.jmb.2006.10.008
  • Primary Citation of Related Structures:  
    2IMW

  • PubMed Abstract: 

    • Numerous template-dependent DNA polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end DNA. Such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses ...

    Numerous template-dependent DNA polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end DNA. Such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. Here, we employed pre-steady state kinetics and X-ray crystallography to establish a mechanism for blunt-end additions catalyzed by Sulfolobus solfataricus Dpo4. Our kinetic studies indicated that the first blunt-end dATP incorporation was 80-fold more efficient than the second, and among natural deoxynucleotides, dATP was the preferred substrate due to its stronger intrahelical base-stacking ability. Such base-stacking contributions are supported by the 41-fold higher ground-state binding affinity of a nucleotide analog, pyrene nucleoside 5'-triphosphate, which lacks hydrogen bonding ability but possesses four conjugated aromatic rings. A 2.05 A resolution structure of Dpo4*(blunt-end DNA)*ddATP revealed that the base and sugar of the incoming ddATP, respectively, stack against the 5'-base of the opposite strand and the 3'-base of the elongating strand. This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation.

    Organizational Affiliation: 

    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVC [auth P]348Saccharolobus solfataricusMutation(s): 0 
Gene Names: dbin
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97W02
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'A [auth S]13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'B [auth T]15N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDS
Query on DDS
Download Ideal Coordinates CCD File 
F [auth P]2',3'-dideoxyadenosine triphosphate
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-NKWVEPMBSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth P],
H [auth P],
I [auth P],
J [auth P],
K [auth P],
G [auth P],
H [auth P],
I [auth P],
J [auth P],
K [auth P],
L [auth P]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth P],
E [auth P]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.057α = 90
b = 101.857β = 90
c = 52.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-10-05 
  • Released Date: 2007-01-16 
    • Deposition Author(s): Ling, H., Yang, W.

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description