9N2K | pdb_00009n2k

N-terminal domain of Bacillus subtilis MutL bound to ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 
    0.196 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.176 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9N2K

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Bacillus subtilis MutL samples multiple conformations during nucleotide binding and hydrolysis.

Rodriguez Gonzalez, J.Davis, C.L.Wilkins, H.Erie, D.A.Guarne, A.

(2026) Structure 34: 530

  • DOI: https://doi.org/10.1016/j.str.2025.12.007
  • Primary Citation Related Structures: 
    9N2K

  • PubMed Abstract: 

    DNA mismatch repair is an evolutionarily conserved repair pathway that corrects replication errors, thereby preventing genome instability. Two evolutionarily conserved proteins, MutS and MutL, recognize the mismatch and mark the newly synthesized strand for repair. Previous studies have shown how bacterial MutS homodimers function asymmetrically to recognize mismatches and recruit MutL. However, whether MutL homodimers also function asymmetrically to coordinate binding to MutS and activation of their nuclease activity remains unclear. Here, we characterize the ATPase domain of Bacillus subtilis MutL, a MutL protein with endonuclease activity, and delineate the differences with Escherichia coli MutL, a homolog without endonuclease activity. We find that B. subtilis MutL has low affinity for ATP and samples a repertoire of conformations that resemble those observed in eukaryotic MutL paralogs, indicating a relationship between ATP-induced dimer compaction and nuclease activity.


  • Organizational Affiliation
    • Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada.

Macromolecule Content 

  • Total Structure Weight: 75.27 kDa 
  • Atom Count: 6,264 
  • Modeled Residue Count: 665 
  • Deposited Residue Count: 670 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA mismatch repair protein MutL
A, B
335Bacillus subtilisMutation(s): 0 
Gene Names: mutLBSU17050
UniProt
Find proteins for P49850 (Bacillus subtilis (strain 168))
Explore P49850 
Go to UniProtKB:  P49850
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49850
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free:  0.196 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.176 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.72α = 90
b = 110.98β = 94.47
c = 57.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references
  • Version 1.2: 2026-03-25
    Changes: Database references