Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48599.50 
• Atom Count: 2942 
• Residue Count: 423 
• Unique protein chains: 1

1JDW

CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRANSFERASE: A MITOCHONDRIAL ENZYME INVOLVED IN CREATINE BIOSYNTHESIS

• DOI: 10.2210/pdb1JDW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 1997-01-22 Released: 1998-01-28 
• Deposition Author(s): Humm, A., Fritsche, E., Steinbacher, S., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 

Literature

Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.

Humm, A., Fritsche, E., Steinbacher, S., Huber, R.

(1997) EMBO J. 16: 3373-3385

• PubMed: 9218780 
• DOI: 10.1093/emboj/16.12.3373
• Primary Citation of Related Structures:  
  4JDW, 3JDW, 2JDW


• PubMed Abstract: 
  

L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine. We have determined the crystal structure of the recombinant human enzyme by multiple isomorphous replacement at 1.9 A resolution. A telluromethionine derivative was used in sequence assignment. The structure of AT reveals a new fold with 5-fold pseudosymmetry of circularly arranged betabeta alphabeta-modules. These enclose the active site compartment, which is accessible only through a narrow channel. The overall structure resembles a basket with handles that are formed from insertions into the betabeta alphabeta-modules. Binding of L-ornithine, a product inhibitor, reveals a marked induced-fit mechanism, with a loop at the active site entrance changing its conformation accompanied by a shift of an alpha-helix by -4 A. Binding of the arginine educt to the inactive mutant C407A shows a similar mode of binding. A reaction mechanism with a catalytic triad Cys-His-Asp is proposed on the basis of substrate and product bound states.

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Related Citations: 

• Bioincorporation of Telluromethionine Into Proteins: A Promising New Approach for X-Ray Structure Analysis of Proteins
  Budisa, N.,Karnbrock, W.,Steinbacher, S.,Humm, A.,Prade, L.,Neuefeind, T.,Moroder, L.,Huber, R.
  (1997) J.Mol.Biol. 270: 616
• Structure and Reaction Mechanism of L-Arginine:Glycine Amidinotransferase
  Humm, A.,Fritsche, E.,Steinbacher, S.
  (1997) Biol.Chem.Hoppe-Seyler 378: 193
• Substrate Binding and Catalysis by L-Arginine:Glycine Amidinotransferase--A Mutagenesis and Crystallographic Study
  Fritsche, E.,Humm, A.,Huber, R.
  (1997) Eur.J.Biochem. 247: 483
• Recombinant Expression and Isolation of Human L-Arginine:Glycine Amidinotransferase and Identification of its Active-Site Cysteine Residue
  Humm, A.,Fritsche, E.,Mann, K.,Gohl, M.,Huber, R.
  (1997) Biochem.J. 322: 771




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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Martinsried, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
L-ARGININE\:GLYCINE AMIDINOTRANSFERASE	A	423	Homo sapiens	Mutation(s): 0  Gene Names: GATM (AGAT) EC: 2.1.4.1
Find proteins for P50440 (Homo sapiens) Go to Gene View: GATM Go to UniProtKB:  P50440

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 83.600	α = 90.00
b = 83.600	β = 90.00
c = 200.400	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
ROTAVATA)	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-01-22 
• Released Date: 1998-01-28 
• Deposition Author(s): Humm, A., Fritsche, E., Steinbacher, S., Huber, R.

Revision History 

• Version 1.0: 1998-01-28
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance