2BKW

Yeast alanine:glyoxylate aminotransferase YFL030w


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

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Ligand Structure Quality Assessment 

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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: https://doi.org/10.1016/j.biochi.2005.09.001
  • Primary Citation of Related Structures:  
    2BKW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALANINE-GLYOXYLATE AMINOTRANSFERASE 1385Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.6.1.44
UniProt
Find proteins for P43567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43567 
Go to UniProtKB:  P43567
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43567
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D 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 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.4α = 90
b = 57.4β = 90
c = 184.5γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
CCP4data scaling
CNSphasing
RESOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

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