3SV3

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T.J., Ordoukhanian, P., Romesberg, F.E., Marx, A.

(2012) Nat Chem Biol 8: 612-614

  • DOI: https://doi.org/10.1038/nchembio.966
  • Primary Citation of Related Structures:  
    3RTV, 3SV3, 3SV4, 3SYZ, 3SZ2

  • PubMed Abstract: 

    Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

    • Organizational Affiliation: 

    Department of Chemistry, Universität Konstanz, Konstanz, Germany.


Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase I, thermostable540Thermus aquaticusMutation(s): 0 
Gene Names: pol I, pol1, polA
EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus)
Explore P19821 
Go to UniProtKB:  P19821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19821
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
(5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')16N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5SI
Query on 5SI
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione
C15 H20 N O12 P3 S
HHAKTXADNAZKDV-BFHYXJOUSA-N
GOL
Query on GOL
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CA [auth C],
G [auth A],
H [auth A],
X [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT
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AA [auth C]
BA [auth C]
DA [auth C]
I [auth A]
J [auth A]
AA [auth C],
BA [auth C],
DA [auth C],
I [auth A],
J [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
Y [auth C],
Z [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG
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F [auth A],
K [auth A],
L [auth A],
Q [auth A],
W [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.545α = 90
b = 108.545β = 90
c = 90.978γ = 120
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references
  • Version 1.2: 2012-09-12
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description