6CST image
Entry Detail
PDB ID:
6CST
Title:
Structure of human DNA polymerase kappa with DNA
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2018-03-21
Release Date:
2019-01-30
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA polymerase kappa
Chain IDs:A, B
Chain Length:551
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')
Chain IDs:C, E (auth: P)
Chain Length:9
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')
Chain IDs:D, F (auth: T)
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct
Primary Citation
2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication.
Sci Rep 8 15125 15125 (2018)
PMID: 30310122 DOI: 10.1038/s41598-018-33371-5

Abstact

Human polymerase kappa (polκ) is a distinct Y-family DNA polymerase with a unique N-terminal N-clasp domain. The N-clasp renders polκ's high efficiency and accuracy in DNA replication and lesion bypass. How N-clasp empowers polκ in replication remains unclear due to the disordering of N-clasp. Here, we present a 2.0-Å resolution crystal structure of a polκ ternary complex with DNA and an incoming nucleotide. The structure-function study reveals an ordered N-clasp domain that brings conserved and functionally important residues in contact with the replicating basepair in the active site and contributes to the nucleotidyl transfer reaction. Particularly, a fully ordered Lys25 from the N-clasp domain is in H-bonding with the α- and γ-phosphates of the incoming nucleotide. K25A mutation reduces the polymerase activity of polκ significantly. This lysine is structurally analogous to a conserved lysine in the A-family DNA polymerases in the closed form. In contrast, Lys25 in the previous structures of polκ does not have any contacts with the incoming nucleotide, resembling an open form of a DNA polymerase. Based on structural and functional similarity, we propose a local open/closed mechanism for polκ in DNA replication catalysis, which mimics the common mechanism for all DNA polymerases.

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