2PL5 | pdb_00002pl5

Crystal Structure of Homoserine O-acetyltransferase from Leptospira interrogans

• PDB DOI: https://doi.org/10.2210/pdb2PL5/pdb

• Classification: TRANSFERASE
• Organism(s): Leptospira interrogans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-04-19 Released: 2007-11-20 
• Deposition Author(s): Liu, L., Wang, M., Wang, Y., Wei, Z., Xu, H., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of homoserine O-acetyltransferase from Leptospira interrogans

Wang, M., Liu, L., Wang, Y., Wei, Z., Zhang, P., Li, Y., Jiang, X., Xu, H., Gong, W.

(2007) Biochem Biophys Res Commun 363: 1050-1056

• PubMed: 17927957 
• DOI: https://doi.org/10.1016/j.bbrc.2007.08.153
• Primary Citation Related Structures: 
  2PL5


• PubMed Abstract: 
  

  Homoserine O-acetyltransferase (HTA, EC 2.3.1.31) initiates methionine biosynthesis pathway by catalyzing the transfer of acetyl group from acetyl-CoA to homoserine. This study reports the crystal structure of HTA from Leptospira interrogans determined at 2.2A resolution using selenomethionyl single-wavelength anomalous diffraction method. HTA is modular and consists of two structurally distinct domains--a core alpha/beta domain containing the catalytic site and a helical bundle called the lid domain. Overall, the structure fold belongs to alpha/beta hydrolase superfamily with the characteristic 'catalytic triad' residues in the active site. Detailed structure analysis showed that the catalytic histidine and serine are both present in two conformations, which may be involved in the catalytic mechanism for acetyl transfer.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, PR China.

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: 40.34 kDa 
• Atom Count: 3,043 
• Modeled Residue Count: 362 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-acetyltransferase	A	366	Leptospira interrogans	Mutation(s): 0  Gene Names: metX EC: 2.3.1.31
UniProt
Find proteins for Q8F4I0 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8F4I0  Go to UniProtKB:  Q8F4I0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.124	α = 90
b = 61.124	β = 90
c = 215.143	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Liu, L., Wang, M., Wang, Y., Wei, Z., Xu, H., Gong, W.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations