Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 95.23 kDa 
• Atom Count: 5448 
• Modelled Residue Count: 694 
• Deposited Residue Count: 860 
• Unique protein chains: 1

3RI6

A Novel Mechanism of Sulfur Transfer Catalyzed by O-Acetylhomoserine Sulfhydrylase in Methionine Biosynthetic Pathway of Wolinella succinogenes

• PDB DOI: 10.2210/pdb3RI6/pdb

• Classification: TRANSFERASE
• Organism(s): Wolinella succinogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-13 Released: 2011-08-17 
• Deposition Author(s): Tran, T.H., Krishnamoorthy, K., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

Literature

A novel mechanism of sulfur transfer catalyzed by O-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of Wolinella succinogenes.

Tran, T.H., Krishnamoorthy, K., Begley, T.P., Ealick, S.E.

(2011) Acta Crystallogr D Biol Crystallogr 67: 831-838

• PubMed: 21931214 
• DOI: 10.1107/S0907444911028010
• Primary Citation of Related Structures:  
  3RI6


• PubMed Abstract: 
  

O-Acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5'-phosphate (PLP) dependent sulfide-utilizing enzyme in the L-cysteine and L-methionine biosynthetic pathways of various enteric bacteria and fungi. OAHS catalyzes the conversion of O-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. However, the source of the sulfur has not been identified and no structures of OAHS have been reported in the literature. Here, the crystal structure of Wolinella succinogenes OAHS (MetY) determined at 2.2 Å resolution is reported. MetY crystallized in space group C2 with two monomers in the asymmetric unit. Size-exclusion chromatography, dynamic light scattering and crystal packing indicate that the biological unit is a tetramer in solution. This is further supported by the crystal structure, in which a tetramer is formed using a combination of noncrystallographic and crystallographic twofold axes. A search for structurally homologous proteins revealed that MetY has the same fold as cystathionine γ-lyase and methionine γ-lyase. The active sites of these enzymes, which are also PLP-dependent, share a high degree of structural similarity, suggesting that MetY belongs to the γ-elimination subclass of the Cys/Met metabolism PLP-dependent family of enzymes. The structure of MetY, together with biochemical data, provides insight into the mechanism of sulfur transfer to a small molecule via a protein thiocarboxylate intermediate.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-ACETYLHOMOSERINE SULFHYDRYLASE	A, B	430	Wolinella succinogenes	Mutation(s): 0  Gene Names: mety, WS1012
UniProt
Find proteins for Q7M9C8 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore Q7M9C8  Go to UniProtKB:  Q7M9C8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.8	α = 90
b = 62.5	β = 120.5
c = 91.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-13 
• Released Date: 2011-08-17 
Deposition Author(s): Tran, T.H., Krishnamoorthy, K., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2011-09-28
  Changes: Database references, Derived calculations
• Version 1.2: 2017-02-08
  Changes: Other
• Version 1.3: 2017-11-08
  Changes: Refinement description