5Z42 | pdb_00005z42

Aquifex aeolicus MutL endonuclease domain with three zinc ions.

• PDB DOI: https://doi.org/10.2210/pdb5Z42/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-10 Released: 2018-04-25 
• Deposition Author(s): Fukui, K., Yano, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus

Fukui, K., Baba, S., Kumasaka, T., Yano, T.

(2018) FEBS Lett 592: 1611-1619

• PubMed: 29645090 
• DOI: https://doi.org/10.1002/1873-3468.13050
• Primary Citation Related Structures: 
  5Z41, 5Z42


• PubMed Abstract: 
  

  The DNA mismatch repair endonuclease MutL consists of N-terminal ATPase and C-terminal endonuclease domains. The endonuclease domain binds zinc ion, although the ion seems not to function as a catalytic metal ion. Here, we solved the crystal structures of the Aquifex aeolicus MutL (aqMutL) endonuclease domain complexed with a single and three zinc ions. Differences between the two structures show that binding of multiple zinc ions induces a closed-to-open conformational change at the catalytic site. It is also revealed that the three-zinc-bound form of the endonuclease domain exhibits higher endonuclease activity than the single-zinc-bound form. These results indicate that multiple zinc ions are required for the proper folding of the endonuclease domain, which would facilitate the endonuclease activity of aqMutL.

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Organizational Affiliation: 
• Department of Biochemistry, Osaka Medical College, Takatsuki, Japan.
Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, gel filtration, cross-linking, light scattering

Macromolecule Content 

• Total Structure Weight: 12.89 kDa 
• Atom Count: 1,014 
• Modeled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein MutL	A	102	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: mutL, aq_1578
UniProt
Find proteins for O67518 (Aquifex aeolicus (strain VF5)) Explore O67518  Go to UniProtKB:  O67518

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.623	α = 90
b = 35.623	β = 90
c = 167.918	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Fukui, K., Yano, T.

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations