7U7F

Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mM Mn2+ for 90s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Literature

In crystallo observation of three metal ion promoted DNA polymerase misincorporation.

Chang, C.Lee Luo, C.Gao, Y.

(2022) Nat Commun 13: 2346-2346

  • DOI: 10.1038/s41467-022-30005-3
  • Primary Citation of Related Structures:  
    7U72, 7U73, 7U74, 7U75, 7U76, 7U77, 7U78, 7U79, 7U7A, 7U7B, 7U7C, 7U7D, 7U7E, 7U7F, 7U7G, 7U7I, 7U7J, 7U7K, 7U7L, 7U7R, 7U7S, 7U7T, 7U7U, 7U7V, 7U7W, 7U7X, 7U7Y, 7U7Z, 7U80, 7U81, 7U82, 7U83, 7U84

  • PubMed Abstract: 
  • Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved ...

    Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.


    Organizational Affiliation

    Department of Biosciences, Rice University, Houston, TX, 77005, USA. yg60@rice.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase etaA435Homo sapiensMutation(s): 0 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y253
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')B [auth T]12synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3')C [auth P]9synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.269α = 90
b = 98.269β = 90
c = 81.983γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR190046
Welch FoundationUnited StatesC-2033-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008280

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references