Biological Assembly 1  

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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: 279603.03 
• Atom Count: 19456 
• Residue Count: 2460 
• Unique protein chains: 1

1MPX

ALPHA-AMINO ACID ESTER HYDROLASE LABELED WITH SELENOMETHIONINE

• DOI: 10.2210/pdb1MPX/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas citri
• Expression System: Escherichia coli


• Deposited: 2002-09-13 Released: 2003-04-15 
• Deposition Author(s): Barends, T.R.M., Polderman-Tijmes, J.J., Jekel, P.A., Hensgens, C.M.H., de Vries, E.J., Janssen, D.B., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.178 
• R-Value Work: 0.149 

Literature

The sequence and crystal structure of the alpha-amino acid ester hydrolase from Xanthomonas citri define a new family of beta-lactam antibiotic acylases.

Barends, T.R., Polderman-Tijmes, J.J., Jekel, P.A., Hensgens, C.M., de Vries, E.J., Janssen, D.B., Dijkstra, B.W.

(2003) J.Biol.Chem. 278: 23076-23084

• PubMed: 12684501 
• DOI: 10.1074/jbc.M302246200


• PubMed Abstract: 
  

alpha-Amino acid ester hydrolases (AEHs) catalyze the hydrolysis and synthesis of esters and amides with an alpha-amino group. As such, they can synthesize beta-lactam antibiotics from acyl compounds and beta-lactam nuclei obtained from the hydrolysis of natural antibiotics. This article describes the gene sequence and the 1.9-A resolution crystal structure of the AEH from Xanthomonas citri. The enzyme consists of an alpha/beta-hydrolase fold domain, a helical cap domain, and a jellyroll beta-domain. Structural homology was observed to the Rhodococcus cocaine esterase, indicating that both enzymes belong to the same class of bacterial hydrolases. Docking of a beta-lactam antibiotic in the active site explains the substrate specificity, specifically the necessity of an alpha-amino group on the substrate, and explains the low specificity toward the beta-lactam nucleus.

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Organizational Affiliation: 

Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
alpha-amino acid ester hydrolase	A, B, C, D	615	Xanthomonas citri	Mutation(s): 0  EC: 3.1.1.43
Find proteins for Q6YBS3 (Xanthomonas citri) Go to UniProtKB:  Q6YBS3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B, C, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.178 
• R-Value Work: 0.149 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 89.772	α = 90.00
b = 126.016	β = 91.06
c = 132.291	γ = 90.00

Software Package:

Software Name	Purpose
SnB	phasing
SOLVE	phasing
SCALEPACK	data scaling
RESOLVE	model building
ARP/wARP	model building
DENZO	data reduction
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-13 
• Released Date: 2003-04-15 
• Deposition Author(s): Barends, T.R.M., Polderman-Tijmes, J.J., Jekel, P.A., Hensgens, C.M.H., de Vries, E.J., Janssen, D.B., Dijkstra, B.W.

Revision History 

• Version 1.0: 2003-04-15
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description