1KCF

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.

Ceschini, S.Keeley, A.McAlister, M.S.Oram, M.Phelan, J.Pearl, L.H.Tsaneva, I.R.Barrett, T.E.

(2001) EMBO J 20: 6601-6611

  • DOI: 10.1093/emboj/20.23.6601
  • Primary Citation of Related Structures:  
    1KCF

  • PubMed Abstract: 
  • Resolution of Holliday junctions into separate DNA duplexes requires enzymatic cleavage of an equivalent strand from each contributing duplex at or close to the point of strand exchange. Diverse Holliday junction-resolving enzymes have been identified in bacteria, bacteriophages, archaea and pox viruses, but the only eukaryotic examples identified so far are those from fungal mitochondria ...

    Resolution of Holliday junctions into separate DNA duplexes requires enzymatic cleavage of an equivalent strand from each contributing duplex at or close to the point of strand exchange. Diverse Holliday junction-resolving enzymes have been identified in bacteria, bacteriophages, archaea and pox viruses, but the only eukaryotic examples identified so far are those from fungal mitochondria. We have now determined the crystal structure of Ydc2 (also known as SpCce1), a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA. This first structure of a eukaryotic Holliday junction resolvase confirms a distant evolutionary relationship to the bacterial RuvC family, but reveals structural features which are unique to the eukaryotic enzymes. Detailed analysis of the dimeric structure suggests mechanisms for junction isomerization and communication between the two active sites, and together with site-directed mutagenesis identifies residues involved in catalysis.


    Organizational Affiliation

    Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I AB258Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPAC25G10.02
EC: 3.1 (PDB Primary Data), 3.1.22.4 (UniProt)
Find proteins for Q10423 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q10423 
Go to UniProtKB:  Q10423
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72α = 90
b = 133.94β = 90
c = 73.25γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
RESOLVEmodel building
CNSrefinement
DENZOdata reduction
CCP4data scaling
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance