3JDW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.181 

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

  • DOI: 10.1093/emboj/16.12.3373
  • Primary Citation of Related Structures:  

  • 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 mu ...

    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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
A
423Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ORN
Query on ORN

Download SDF File 
Download CCD File 
A
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ORNKi: 253000 nM BINDINGMOAD
ORNKi: 253000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.760α = 90.00
b = 83.760β = 90.00
c = 199.650γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
X-PLORmodel building
ROTAVATA)data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance