6AS7

CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF HUMAN DNA POLYMERASE ALPHA IN TERNARY COMPLEX WITH AN DNA-PRIMED DNA TEMPLATE AND DCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.259 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Activity and fidelity of human DNA polymerase alpha depend on primer structure.

Baranovskiy, A.G.Duong, V.N.Babayeva, N.D.Zhang, Y.Pavlov, Y.I.Anderson, K.S.Tahirov, T.H.

(2018) J Biol Chem 293: 6824-6843

  • DOI: https://doi.org/10.1074/jbc.RA117.001074
  • Primary Citation of Related Structures:  
    6AS7

  • PubMed Abstract: 

    DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Polα is in the open conformation. Polα induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Polα extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Polα has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Polα with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.


  • Organizational Affiliation

    From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit922Homo sapiensMutation(s): 1 
Gene Names: POLA1POLA
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
PHAROS:  P09884
GTEx:  ENSG00000101868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09884
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*CP*TP*GP*GP*AP*GP*CP*GP*C)-3')11unidentified
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*GP*CP*GP*CP*TP*CP*CP*AP*GP*GP*C)-3')13unidentified
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.259 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.807α = 90
b = 151.807β = 90
c = 113.299γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM101167
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA036727
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description