5Z42

Aquifex aeolicus MutL endonuclease domain with three zinc ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/1873-3468.13050
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biochemistry, Osaka Medical College, Takatsuki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein MutL102Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: mutLaq_1578
UniProt
Find proteins for O67518 (Aquifex aeolicus (strain VF5))
Explore O67518 
Go to UniProtKB:  O67518
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67518
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
I [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.623α = 90
b = 35.623β = 90
c = 167.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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