2BKW | pdb_00002bkw

Yeast alanine:glyoxylate aminotransferase YFL030w

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.258 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 42.6 kDa 
  • Atom Count: 3,028 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 385 
  • Unique protein chains: 1

Macromolecules

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|  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
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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), 0.251 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.197 (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

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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
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary