Crystal Structure of PMS2 with Substrate

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


PMS2 variant results in loss of ATPase activity without compromising mismatch repair.

D'Arcy, B.M.Arrington, J.Weisman, J.McClellan, S.B.Yang, Z.Deivanayagam, C.Blount, J.Prakash, A.

(2022) Mol Genet Genomic Med 10: e1908-e1908

  • DOI: https://doi.org/10.1002/mgg3.1908
  • Primary Citation of Related Structures:  
    7RCB, 7RCI, 7RCK

  • PubMed Abstract: 

    Hereditary cancer syndromes account for approximately 5%-10% of all diagnosed cancer cases. Lynch syndrome (LS) is an autosomal dominant hereditary cancer condition that predisposes individuals to an elevated lifetime risk for developing colorectal, endometrial, and other cancers. LS results from a pathogenic mutation in one of four mismatch repair (MMR) genes (MSH2, MSH6, MLH1, and PMS2). The diagnosis of LS is often challenged by the identification of missense mutations, termed variants of uncertain significance, whose functional effect on the protein is not known. Of the eight PMS2 variants initially selected for this study, we identified a variant within the N-terminal domain where asparagine 335 is mutated to serine, p.Asn335Ser, which lacked ATPase activity, yet appears to be proficient in MMR. To expand our understanding of this functional dichotomy, we performed biophysical and structural studies, and noted that p.Asn335Ser binds to ATP but is unable to hydrolyze it to ADP. To examine the impact of p.Asn335Ser on MMR, we developed a novel in-cell fluorescent-based microsatellite instability reporter that revealed p.Asn335Ser maintained genomic stability. We conclude that in the absence of gross structural changes, PMS2 ATP hydrolysis is not necessary for proficient MMR and that the ATPase deficient p.Asn335Ser variant is likely benign.

  • Organizational Affiliation

    Mitchell Cancer Institute, University of South Alabama Health, Mobile, Alabama, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mismatch repair endonuclease PMS2
A, B
365Homo sapiensMutation(s): 0 
Gene Names: PMS2PMSL2
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54278 (Homo sapiens)
Explore P54278 
Go to UniProtKB:  P54278
PHAROS:  P54278
GTEx:  ENSG00000122512 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54278
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.684α = 90
b = 75.385β = 90
c = 135.313γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description