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.

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-acetyltransferase	A, B, C, D, E 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), 3.1.1.113 (UniProt)
UniProt
Find proteins for Q0MRG5 (Pseudomonas veronii) Explore Q0MRG5 Go to UniProtKB: Q0MRG5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0MRG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain N [auth A] SDF format, chain SA [auth F] SDF format, chain CA [auth C] SDF format, chain QA [auth F] SDF format, chain RA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F]	BA [auth C] CA [auth C] HA [auth D] IA [auth D] N [auth A] 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		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth C]	AA [auth C] EA [auth D] FA [auth D] G [auth A] GA [auth D] 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		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain JA [auth D] SDF format, chain MA [auth E] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain NA [auth E] SDF format, chain O [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth A]	DA [auth C] JA [auth D] MA [auth E] NA [auth E] O [auth A] 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		Interactions Focus chain DA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain O [auth A] Focus chain TA [auth F] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain O [auth A] Focus chain TA [auth F] Focus chain U [auth B]