2FCO | pdb_00002fco

Crystal Structure of Bacillus stearothermophilus PrfA-Holliday Junction Resolvase

• PDB DOI: https://doi.org/10.2210/pdb2FCO/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-12 Released: 2006-11-21 
• Deposition Author(s): Li, J., Jedrzejas, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase.

Kelly, S.J., Li, J., Setlow, P., Jedrzejas, M.J.

(2007) Proteins 68: 961-971

• PubMed: 17557334 
• DOI: https://doi.org/10.1002/prot.21418
• Primary Citation Related Structures: 
  2FCO


• PubMed Abstract: 
  

  Here we report a high resolution structure of RecU-Holliday junction resolvase from Bacillus stearothermophilus. The functional unit of RecU is a homodimer that contains a "mushroom" like structure with a rigid cap and two highly flexible loops extending outwards. These loops appear to be highly flexible/dynamic, and presumably are directly involved in DNA binding and holding it for catalysis. Structural modifications of both the protein and DNA upon their interaction are essential for catalysis. An Mg2+ ion is present in each of the two active sites in this homodimeric enzyme, and two water molecules are coordinated with each Mg2+ ion. Our data are consistent with one of these water molecules acting as a nucleophile and the other as a general acid. The identities of the general base and general acid involved in catalysis and the Lewis acid that stabilizes the pentacovalent transition state phosphate ion are proposed. A model for the RecU-Holliday junction DNA complex is also proposed and discussed in the context of DNA binding and cleavage.

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Organizational Affiliation: 
• Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.

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: 46.32 kDa 
• Atom Count: 2,958 
• Modeled Residue Count: 308 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
recombination protein U (penicillin-binding protein related factor A)	A, B	200	Geobacillus kaustophilus HTA426	Mutation(s): 0  Gene Names: RecU/PrfA EC: 3.1.22.4 (PDB Primary Data), 3.1.21.10 (UniProt)
UniProt
Find proteins for Q5KXY4 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KXY4  Go to UniProtKB:  Q5KXY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.886	α = 90
b = 96.886	β = 90
c = 114.539	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Li, J., Jedrzejas, M.J.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2007-11-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations