9KCE | pdb_00009kce

Crystal Structure of the ATP analog-bound closed state of Thermotoga maritima MutS2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

ATP binding controls the molecular function of bacterial MutS2 by mediating closure of the dimeric clamp structure.

Fukui, K.Murakawa, T.Hino, N.Kondo, N.Yano, T.

(2025) Structure 33: 1007-1015.e4

  • DOI: https://doi.org/10.1016/j.str.2025.03.003
  • Primary Citation Related Structures: 
    9KCE

  • PubMed Abstract: 

    MutS2 recognizes branched DNA structures to regulate homologous recombination. MutS2 also has a role in ribosome recycling, where it resolves collided ribosomes. These functions require ATP-dependent conformational changes of MutS2. In the known nucleotide-free and ADP-bound MutS2 structures the dimeric clamp-like structure adopts open conformations. Here, we present the crystal structure of MutS2 with a bound ATP analog revealing a closed conformation of the clamp. Experiments with MutS2, where an unnatural photo-crosslinking capable amino acid was introduced into the clamp revealed that ATP-dependent closure also occurs in solution. Binding of MutS2 to a terminal-containing DNA was not affected by ATP, whereas that to a terminal-less DNA was reinforced. These findings suggest that clamp closure enables MutS2 to stay bound to recombination intermediates, which might regulate recombination. Furthermore, closure of the clamp provides insights into the mechanism of dissociation of collided ribosomes mediated by MutS2.


  • Organizational Affiliation
    • Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan. Electronic address: kenji.fukui@ompu.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 230.01 kDa 
  • Atom Count: 15,522 
  • Modeled Residue Count: 1,963 
  • Deposited Residue Count: 1,988 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endonuclease MutS2A [auth B],
B [auth C],
C [auth A],
D
497Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: mutS2mutSBTM_1278
EC: 3.1 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q9X105 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X105 
Go to UniProtKB:  Q9X105
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X105
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
(Subject of Investigation/LOI)

Query on ANP



Download:Ideal Coordinates CCD File
E [auth B],
J [auth C],
Q [auth A],
W [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth B]
H [auth B]
I [auth B]
L [auth C]
M [auth C]
G [auth B],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
T [auth A],
U [auth A],
V [auth A],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
X [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
F [auth B],
K [auth C],
R [auth A],
S [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.74α = 90
b = 142.85β = 105.39
c = 139.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24K08718

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release