2BKW

Yeast alanine:glyoxylate aminotransferase YFL030w

• PDB DOI: https://doi.org/10.2210/pdb2BKW/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-02-21 Released: 2005-11-02 
• Deposition Author(s): Meyer, P., Liger, D., Leulliot, N., Quevillon-Cheruel, S., Zhou, C.Z., Borel, F., Ferrer, J.L., Poupon, A., Janin, J., van Tilbeurgh, H.

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Experimental Data Snapshot

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

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

• PubMed: 16226833 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALANINE-GLYOXYLATE AMINOTRANSFERASE 1	A	385	Saccharomyces cerevisiae S288C	Mutation(s): 0  EC: 2.6.1.44
UniProt
Find proteins for P43567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43567  Go to UniProtKB:  P43567

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLV	C [auth A]	GLYOXYLIC ACID C2 H2 O3 HHLFWLYXYJOTON-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.258 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.4	α = 90
b = 57.4	β = 90
c = 184.5	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
CCP4	data scaling
CNS	phasing
RESOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-02 
Deposition Author(s): Meyer, P., Liger, D., Leulliot, N., Quevillon-Cheruel, S., Zhou, C.Z., Borel, F., Ferrer, J.L., Poupon, A., Janin, J., van Tilbeurgh, H.

Revision History  

• 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