5YTE

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Unnatural cytosine bases recognized as thymines by DNA polymerases via the formation of the Watson-Crick geometry.

Yi, C.Zeng, H.Mondal, M.Song, R.Zhang, J.Xia, B.Liu, M.Zhu, C.He, B.Gao, Y.Q.

(2018) Angew. Chem. Int. Ed. Engl. --: --

  • DOI: 10.1002/anie.201807845
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms how DNA polymerases faithfully decode chemical information on the template. For instance, we previously showed that two unnatural cytosine bases (termed "M-fC" an ...

    The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms how DNA polymerases faithfully decode chemical information on the template. For instance, we previously showed that two unnatural cytosine bases (termed "M-fC" and "I-fC"), which are chemical labeling adducts of the epigenetic base 5-formylcytosine, can induce C-to-T transition during DNA amplification. However, how DNA polymerases recognize such unnatural cytosine bases remain enigmatic. Herein, we determined crystal structures of the unnatural cytosine bases pairing to dA/dG in the KlenTaq-host-guest complex system and pairing to dATP in the active site. The results show that both M-fC and I-fC base pair with dA/dATP, but not with dG, in a Watson-Crick geometry. Our study reveals that the formation of the Watson-Crick geometry, which may be enabled by the A-rule, is important for the recognition of unnatural cytosines, and this expands the current understanding of unnatural base recognition by DNA polymerases.


    Organizational Affiliation

    Peking University, School of Life Sciences, 5 Yiheyuan Road, 100871, Beijing, CHINA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I, thermostable
A
539Thermus aquaticusMutation(s): 0 
Gene Names: polA (pol1)
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Go to UniProtKB:  P19821
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')B12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C16synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.169α = 90.00
b = 109.169β = 90.00
c = 91.003γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Basic Research Foundation of China GrantChina2014CB964900
the National Natural Science Foundation of China GrantsChina31270838 and 21522201

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release