Crystal Structure of N terminal domain of a DNA repair protein

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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Functional residues on the surface of the N-terminal domain of yeast Pms1.

Arana, M.E.Holmes, S.F.Fortune, J.M.Moon, A.F.Pedersen, L.C.Kunkel, T.A.

(2010) DNA Repair (Amst) 9: 448-457

  • DOI: https://doi.org/10.1016/j.dnarep.2010.01.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Saccharomyces cerevisiae MutLalpha is a heterodimer of Mlh1 and Pms1 that participates in DNA mismatch repair (MMR). Both proteins have weakly conserved C-terminal regions (CTDs), with the CTD of Pms1 harboring an essential endonuclease activity. These proteins also have conserved N-terminal domains (NTDs) that bind and hydrolyze ATP and bind to DNA. To better understand Pms1 functions and potential interactions with DNA and/or other proteins, we solved the 2.5A crystal structure of yeast Pms1 (yPms1) NTD. The structure is similar to the homologous NTDs of Escherichia coli MutL and human PMS2, including the site involved in ATP binding and hydrolysis. The structure reveals a number of conserved, positively charged surface residues that do not interact with other residues in the NTD and are therefore candidates for interactions with DNA, with the CTD and/or with other proteins. When these were replaced with glutamate, several replacements resulted in yeast strains with elevated mutation rates. Two replacements also resulted in NTDs with decreased DNA binding affinity in vitro, suggesting that these residues contribute to DNA binding that is important for mismatch repair. Elevated mutation rates also resulted from surface residue replacements that did not affect DNA binding, suggesting that these conserved residues serve other functions, possibly involving interactions with other MMR proteins.

  • Organizational Affiliation

    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein PMS1
A, B
367Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PMS1
Find proteins for P14242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14242 
Go to UniProtKB:  P14242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14242
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.592α = 90
b = 103.288β = 90
c = 117.167γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description