Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 60.69 kDa 
• Atom Count: 3968 
• Modelled Residue Count: 468 
• Deposited Residue Count: 516 
• Unique protein chains: 1

1KCF

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2

• PDB DOI: 10.2210/pdb1KCF/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-11-08 Released: 2001-11-28 
• Deposition Author(s): Ceschini, S., Keeley, A., McAlister, M.S.B., Oram, M., Phelan, J., Pearl, L.H., Tsaneva, I.R., Barrett, T.E.

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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 

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

• PubMed: 11726496 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I	A, B	258	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: SPAC25G10.02 EC: 3.1 (PDB Primary Data), 3.1.22.4 (UniProt)
UniProt
Find proteins for Q10423 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10423  Go to UniProtKB:  Q10423

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 72	α = 90
b = 133.94	β = 90
c = 73.25	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	model building
CNS	refinement
DENZO	data reduction
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-08 
• Released Date: 2001-11-28 
Deposition Author(s): Ceschini, S., Keeley, A., McAlister, M.S.B., Oram, M., Phelan, J., Pearl, L.H., Tsaneva, I.R., Barrett, T.E.

Revision History  

• 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