1JDX

CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH L-NORVALINE


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study.

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

(1999) J.Biol.Chem. 274: 3026-3032

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and H ...

    Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate the structural basis of these induced-fit movements, the x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid, as well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved at 2.6-, 2.5-, 2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize the open conformer. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-fit mechanism. Helix H9 does not add to the stability of the protein.


    Organizational Affiliation

    Department of Structural Research, Max Planck Institute for Biochemistry, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE)
A
386Homo 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
NVA
Query on NVA

Download SDF File 
Download CCD File 
A
NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.800α = 90.00
b = 83.800β = 90.00
c = 199.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
CCP4data scaling
ROTAVATAdata scaling
MOSFLMdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description