4AZD

T57V mutant of aspartate decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb4AZD/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-06-25 Released: 2012-07-25 
• Deposition Author(s): Webb, M.E., Yorke, B.A., Kershaw, T., Lovelock, S., Lobley, C.M.C., Kilkenny, M.L., Smith, A.G., Blundell, T.L., Pearson, A.R., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Threonine 57 is Required for the Post-Translational Activation of Escherichia Coli Aspartate Alpha-Decarboxylase

Webb, M.E., Yorke, B.A., Kershaw, T., Lovelock, S., Lobley, C.M.C., Kilkenny, M.L., Smith, A.G., Blundell, T.L., Pearson, A.R., Abell, C.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1166

• PubMed: 24699660 
• DOI: https://doi.org/10.1107/S1399004713034275
• Primary Citation of Related Structures:  
  4AZD


• PubMed Abstract: 
  

  Aspartate α-decarboxylase is a pyruvoyl-dependent decarboxylase required for the production of β-alanine in the bacterial pantothenate (vitamin B5) biosynthesis pathway. The pyruvoyl group is formed via the intramolecular rearrangement of a serine residue to generate a backbone ester intermediate which is cleaved to generate an N-terminal pyruvoyl group. Site-directed mutagenesis of residues adjacent to the active site, including Tyr22, Thr57 and Tyr58, reveals that only mutation of Thr57 leads to changes in the degree of post-translational activation. The crystal structure of the site-directed mutant T57V is consistent with a non-rearranged backbone, supporting the hypothesis that Thr57 is required for the formation of the ester intermediate in activation.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 31.96 kDa 
• Atom Count: 2,021 
• Modelled Residue Count: 239 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE	A, B	143	Escherichia coli K-12	Mutation(s): 1  EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790  Go to UniProtKB:  P0A790

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], D [auth A], E [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.92	α = 90
b = 69.92	β = 90
c = 217.72	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Webb, M.E., Yorke, B.A., Kershaw, T., Lovelock, S., Lobley, C.M.C., Kilkenny, M.L., Smith, A.G., Blundell, T.L., Pearson, A.R., Abell, C.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2014-04-16
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description