Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.72 kDa 
• Atom Count: 7528 
• Modelled Residue Count: 818 
• Deposited Residue Count: 820 
• Unique protein chains: 1

1S9R

CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A REACTION INTERMEDIATE

• PDB DOI: 10.2210/pdb1S9R/pdb

• Classification: HYDROLASE
• Organism(s): Mycoplasmopsis arginini
• Mutation(s): No 


• Deposited: 2004-02-05 Released: 2004-04-13 
• Deposition Author(s): Das, K., Buttler, G.H., Kwiatkowski, V., Clark Jr., A.D., Yadav, P., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Literature

Crystal Structures of Arginine Deiminase with Covalent Reaction Intermediates: Implications for Catalytic Mechanism

Das, K., Buttler, G.H., Kwiatkowski, V., Clark Jr., A.D., Yadav, P., Arnold, E.

(2004) Structure 12: 657-667

• PubMed: 15062088 
• DOI: 10.1016/j.str.2004.02.017
• Primary Citation of Related Structures:  
  1LXY, 1S9R


• PubMed Abstract: 
  

Arginine deiminase (ADI), an enzyme that hydrolyzes arginine to generate energy in many parasitic microorganisms, has potent anticancer activities and can halt growth of solid tumors. We determined the crystal structure of ADI from Mycoplasma arginini in two different forms (1.6 and 2.0 A resolution) using multiple isomorphous replacement. ADI shares common structural features with the arginine-catabolizing enzymes Arg:Gly amidinotransferase and dimethylarginine dimethyl-aminohydrolase; ADI contains an additional domain of five helices. The scissile C-N bonds of the substrates and the catalytic triads (Cys398-His269-Glu213 of ADI) for the three enzymes superimpose on each other. The ADI structure from form I crystals corresponds to a tetrahedral intermediate with four heteroatoms (1S, 2N, 1O) covalently bonded to the reaction-center carbon. The structure from form II crystals represents an amidino-enzyme complex; the reaction-center carbon is covalently bonded to Cys398 sulfur and two nitrogens, and the reacting water molecule is only 2.54 A away.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine (CABM) and Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854 USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine deiminase	A, B	410	Mycoplasmopsis arginini	Mutation(s): 0  Gene Names: arcA EC: 3.5.3.6
UniProt
Find proteins for P23793 (Mycoplasmopsis arginini) Explore P23793  Go to UniProtKB:  P23793

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	C [auth A], I [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
TRS	D [auth A], J [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
UNX	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.83	α = 90
b = 76.36	β = 107.96
c = 82.85	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-05 
• Released Date: 2004-04-13 
Deposition Author(s): Das, K., Buttler, G.H., Kwiatkowski, V., Clark Jr., A.D., Yadav, P., Arnold, E.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance