5EFZ

Monoclinic structure of the acetyl esterase MekB

• PDB DOI:  https://doi.org/10.2210/pdb5EFZ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas veronii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-26 Released: 2015-12-16 
• Deposition Author(s): Toelzer, C., Pal, S., Watzlawick, H., Altenbuchner, J., Niefind, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.196 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Literature

A novel esterase subfamily with alpha / beta-hydrolase fold suggested by structures of two bacterial enzymes homologous to l-homoserine O-acetyl transferases.

Tolzer, C., Pal, S., Watzlawick, H., Altenbuchner, J., Niefind, K.

(2016) FEBS Lett 590: 174-184

• PubMed: 26787467 
• DOI: https://doi.org/10.1002/1873-3468.12031
• Primary Citation of Related Structures:  
  5D6O, 5D7B, 5E4Y, 5EFZ


• PubMed Abstract: 
  

MekB from Pseudomonas veronii and CgHle from Corynebacteriumglutamicum belong to the superfamily of α/β-hydrolase fold proteins. Based on sequence comparisons, they are annotated as homoserine transacetylases in popular databases like UNIPROT, PFAM or ESTHER. However, experimentally, MekB and CgHle were shown to be esterases that hydrolyse preferentially acetic acid esters. We describe the x-ray structures of these enzymes solved to high resolution. The overall structures confirm the close relatedness to experimentally validated homoserine acetyl transferases, but simultaneously the structures exclude the ability of MekB and CgHle to bind homoserine and acetyl-CoA. Insofar the MekB and CgHle structures suggest dividing the homoserine transacetylase family into subfamilies, namely genuine acetyl transferases and acetyl esterases with MekB and CgHle as constituting members of the latter.

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Organizational Affiliation: 

Department für Chemie, Institut für Biochemie, Universität zu Köln, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 241.18 kDa 
• Atom Count: 17,233 
• Modelled Residue Count: 2,068 
• Deposited Residue Count: 2,166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-acetyltransferase	A, B, C, D, E, F	361	Pseudomonas veronii	Mutation(s): 0  Gene Names: mekB EC: 2.3.1 (PDB Primary Data), 2.3.1.31 (PDB Primary Data)
UniProt
Find proteins for Q0MRG5 (Pseudomonas veronii) Explore Q0MRG5  Go to UniProtKB:  Q0MRG5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	BA [auth C], CA [auth C], HA [auth D], IA [auth D], N [auth A], QA [auth F], RA [auth F], SA [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth C], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], OA [auth F], P [auth B], PA [auth F], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	DA [auth C], JA [auth D], MA [auth E], NA [auth E], O [auth A], TA [auth F], U [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.196 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.848	α = 90
b = 110.342	β = 106.89
c = 122.817	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Toelzer, C., Pal, S., Watzlawick, H., Altenbuchner, J., Niefind, K.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release