7P8V | pdb_00007p8v

The structure of E. coli MutL bound to a 3' resected DNA end

• PDB DOI: https://doi.org/10.2210/pdb7P8V/pdb
• NAKB: 7P8V
• EM Map EMD-13255: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli K-12, DNA molecule
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-23 Released: 2022-06-29 
• Deposition Author(s): Borsellini, A., Lamers, M.H.
• Funding Organization(s): Marie Sklodowska-Curie Actions, FragNET ITN

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

MutL binds to 3' resected DNA ends and blocks DNA polymerase access.

Borsellini, A., Lebbink, J.H.G., Lamers, M.H.

(2022) Nucleic Acids Res 50: 6224-6234

• PubMed: 35670670 
• DOI: https://doi.org/10.1093/nar/gkac432
• Primary Citation Related Structures: 
  7P8V


• PubMed Abstract: 
  

  DNA mismatch repair removes mis-incorporated bases after DNA replication and reduces the error rate a 100-1000-fold. After recognition of a mismatch, a large section of up to a thousand nucleotides is removed from the daughter strand followed by re-synthesis. How these opposite activities are coordinated is poorly understood. Here we show that the Escherichia coli MutL protein binds to the 3' end of the resected strand and blocks access of Pol I and Pol III. The cryo-EM structure of an 85-kDa MutL-DNA complex, determined to 3.7 Å resolution, reveals a unique DNA binding mode that positions MutL at the 3' end of a primer-template, but not at a 5' resected DNA end or a blunt DNA end. Hence, our work reveals a novel role for MutL in the final stages of mismatch repair by preventing premature DNA synthesis during removal of the mismatched strand.

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Organizational Affiliation: 
• Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 147.86 kDa 
• Atom Count: 5,988 
• Modeled Residue Count: 697 
• Deposited Residue Count: 1,265 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein MutL	A, B	615	Escherichia coli K-12	Mutation(s): 0  Gene Names: mutL, b4170, JW4128
UniProt
Find proteins for P23367 (Escherichia coli (strain K12)) Explore P23367  Go to UniProtKB:  P23367

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template strand	C	22	DNA molecule

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Primer strand	D	13	DNA molecule

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], H [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	F [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Borsellini, A., Lamers, M.H.

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Funding Organization	Location	Grant Number
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	--

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2024-07-17
  Changes: Data collection, Refinement description