2B61 | pdb_00002b61

Crystal Structure of Homoserine Transacetylase

• PDB DOI: https://doi.org/10.2210/pdb2B61/pdb

• Classification: TRANSFERASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-09-29 Released: 2005-11-15 
• Deposition Author(s): Mirza, I.A., Nazi, I., Korczynska, M., Wright, G.D., Berghuis, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal Structure of Homoserine Transacetylase from Haemophilus influenzae Reveals a New Family of alpha/beta-Hydrolases

Mirza, I.A., Nazi, I., Korczynska, M., Wright, G.D., Berghuis, A.M.

(2005) Biochemistry 44: 15768-15773

• PubMed: 16313180 
• DOI: https://doi.org/10.1021/bi051951y
• Primary Citation Related Structures: 
  2B61


• PubMed Abstract: 
  

  Homoserine transacetylase catalyzes one of the required steps in the biosynthesis of methionine in fungi and several bacteria. We have determined the crystal structure of homoserine transacetylase from Haemophilus influenzae to a resolution of 1.65 A. The structure identifies this enzyme to be a member of the alpha/beta-hydrolase structural superfamily. The active site of the enzyme is located near the end of a deep tunnel formed by the juxtaposition of two domains and incorporates a catalytic triad involving Ser143, His337, and Asp304. A structural basis is given for the observed double displacement kinetic mechanism of homoserine transacetylase. Furthermore, the properties of the tunnel provide a rationale for how homoserine transacetylase catalyzes a transferase reaction vs hydrolysis, despite extensive similarity in active site architecture to hydrolytic enzymes.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A4.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.54 kDa 
• Atom Count: 3,272 
• Modeled Residue Count: 357 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-acetyltransferase	A	377	Haemophilus influenzae	Mutation(s): 8  Gene Names: metX, met2 EC: 2.3.1.31
UniProt
Find proteins for P45131 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P45131  Go to UniProtKB:  P45131

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.264	α = 90
b = 85.264	β = 90
c = 120.263	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-15 
Deposition Author(s): Mirza, I.A., Nazi, I., Korczynska, M., Wright, G.D., Berghuis, A.M.

Revision History  

• Version 1.0: 2005-11-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-02-07
  Changes: Experimental preparation
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary