2VYC

Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structure of the Acid Induced Arginine Decarboxylase from Escherichia Coli: Reversible Decamer Assembly Controls Enzyme Activity.

Andrell, J., Hicks, M.G., Palmer, T., Carpenter, E.P., Iwata, S., Maher, M.J.

(2009) Biochemistry 48: 3915

  • DOI: 10.1021/bi900075d

  • PubMed Abstract: 

    • The acid-induced arginine decarboxylase is part of an enzymatic system in Escherichia coli that contributes to making this organism acid resistant. The arginine decarboxylase is a vitamin B(6)-dependent enzyme that is active at acidic pH. It consumes ...

    The acid-induced arginine decarboxylase is part of an enzymatic system in Escherichia coli that contributes to making this organism acid resistant. The arginine decarboxylase is a vitamin B(6)-dependent enzyme that is active at acidic pH. It consumes a proton in the decarboxylation of arginine to agmatine, and by working in tandem with an arginine-agmatine antiporter, this enzymatic cycle protects the organism by preventing the accumulation of protons inside the cell. We have determined the structure of the acid-induced arginine decarboxylase by X-ray crystallography to 2.4 A resolution. The arginine decarboxylase structure revealed a ca. 800 kDa decamer composed as a pentamer of five homodimers. Each homodimer has an abundance of acidic surface residues, which at neutral pH prevents inactive homodimers from associating into active decamers. Conversely, acidic conditions favor the assembly of active decamers. Therefore, the structure of arginine decarboxylase presents a mechanism by which its activity is modulated by external pH.

    Organizational Affiliation: 

    Division of Molecular Biosciences, Imperial College, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIODEGRADATIVE ARGININE DECARBOXYLASE
A, B, C, D, E, F, G, H, I, J
755Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: adiA (adi)
EC: 4.1.1.19
Find proteins for P28629 (Escherichia coli (strain K12))
Go to UniProtKB:  P28629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 197.651α = 90.00
b = 197.651β = 90.00
c = 450.322γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-10-12
    Type: Database references, Derived calculations, Other, Structure summary
  • Version 1.3: 2015-12-02
    Type: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary