2BKW

Yeast alanine:glyoxylate aminotransferase YFL030w


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure and Confirmation of the Alanine:Glyoxylate Aminotransferase Activity of the Yfl030W Yeast Protein

Meyer, P.Liger, D.Leulliot, N.Quevillon-Cheruel, S.Zhou, C.Z.Borel, F.Ferrer, J.L.Poupon, A.Janin, J.Van Tilbeurgh, H.

(2005) Biochimie 87: 1041

  • DOI: 10.1016/j.biochi.2005.09.001

  • PubMed Abstract: 
  • We have determined the three-dimensional crystal structure of the protein encoded by the open reading frame YFL030w from Saccharomyces cerevisiae to a resolution of 2.6 A using single wavelength anomalous diffraction. YFL030w is a 385 amino-acid prot ...

    We have determined the three-dimensional crystal structure of the protein encoded by the open reading frame YFL030w from Saccharomyces cerevisiae to a resolution of 2.6 A using single wavelength anomalous diffraction. YFL030w is a 385 amino-acid protein with sequence similarity to the aminotransferase family. The structure of the protein reveals a homodimer adopting the fold-type I of pyridoxal 5'-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure. The protein shows close structural resemblance with the human alanine:glyoxylate aminotransferase (EC 2.6.1.44), an enzyme involved in the hereditary kidney stone disease primary hyperoxaluria type 1. In this paper we show that YFL030w codes for an alanine:glyoxylate aminotransferase, highly specific for its amino donor and acceptor substrates.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales (CNRS-UPR 9063) Bât. 34, 1, avenue de la Terrasse, 91198 Gif sur Yvette cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
A
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: AGX1
EC: 2.6.1.44
Find proteins for P43567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43567
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLV
Query on GLV

Download SDF File 
Download CCD File 
A
GLYOXYLIC ACID
GLYOXALATE, GLYOXYLATE
C2 H2 O3
HHLFWLYXYJOTON-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.400α = 90.00
b = 57.400β = 90.00
c = 184.500γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
XDSdata reduction
CCP4data scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-02
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance