4E4W | pdb_00004e4w

Structure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1) heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.210 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4E4W

This is version 1.3 of the entry. See complete history

Literature

Structure of the MutLalpha C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site.

Gueneau, E.Dherin, C.Legrand, P.Tellier-Lebegue, C.Gilquin, B.Bonnesoeur, P.Londino, F.Quemener, C.Le Du, M.H.Marquez, J.A.Moutiez, M.Gondry, M.Boiteux, S.Charbonnier, J.B.

(2013) Nat Struct Mol Biol 20: 461-468

  • DOI: https://doi.org/10.1038/nsmb.2511
  • Primary Citation Related Structures: 
    4E4W, 4FMN, 4FMO

  • PubMed Abstract: 

    Mismatch-repair factors have a prominent role in surveying eukaryotic DNA-replication fidelity and in ensuring correct meiotic recombination. These functions depend on MutL-homolog heterodimers with Mlh1. In humans, MLH1 mutations underlie half of hereditary nonpolyposis colorectal cancers (HNPCCs). Here we report crystal structures of the MutLα (Mlh1-Pms1 heterodimer) C-terminal domain (CTD) from Saccharomyces cerevisiae, alone and in complex with fragments derived from Mlh1 partners. These structures reveal structural rearrangements and additional domains in MutLα as compared to the bacterial MutL counterparts and show that the strictly conserved C terminus of Mlh1 forms part of the Pms1 endonuclease site. The structures of the ternary complexes between MutLα(CTD) and Exo1 or Ntg2 fragments reveal the binding mode of the MIP-box motif shared by several Mlh1 partners. Finally, the structures provide a rationale for the deleterious impact of MLH1 mutations in HNPCCs.


  • Organizational Affiliation
    • Unité Mixte de Recherche 8221, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institut de Biologie et Technologies de Saclay, Gif-sur-Yvette, France.

Macromolecule Content 

  • Total Structure Weight: 61.65 kDa 
  • Atom Count: 4,032 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 524 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA mismatch repair protein MLH1285Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MLH1PMS2YMR167WYM8520.16
UniProt
Find proteins for P38920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38920 
Go to UniProtKB:  P38920
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38920
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA mismatch repair protein PMS1239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PMS1YNL082WN2317
UniProt
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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.210 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.21α = 90
b = 66.14β = 90.75
c = 74.01γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SHELXSphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations