4AZD | pdb_00004azd

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 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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 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.
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, England.
School of Chemistry, University of Leeds, Leeds LS2 9JT, England.
Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, England.
University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, 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 
• Modeled 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 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

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