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
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.231
R-Value Work: 0.196
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1093/emboj/16.12.3373
Primary Citation of Related Structures:
3JDW, 4JDW, 2JDW, 1JDW

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.

Related Citations:

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

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ARGININE\:GLYCINE AMIDINOTRANSFERASE	A	423	Homo sapiens	Mutation(s): 0 Gene Names: AT38H, GATM, AGAT EC: 2.1.4.1
Find proteins for P50440 (Homo sapiens) Explore P50440 Go to UniProtKB: P50440
NIH Common Fund Data Resources
PHAROS: P50440 GTEx: ENSG00000171766
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Ligand Interaction