1XE8 | pdb_00001xe8

Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly roll fold.

• PDB DOI: https://doi.org/10.2210/pdb1XE8/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-09-09 Released: 2005-01-11 
• Deposition Author(s): Zhou, C.-Z., Meyer, P., Quevillon-Cheruel, S., Li de La Sierra-Gallay, I., Collinet, B., Graille, M., Leulliot, N., Sorel, I., Janin, J., Van Tilbeurgh, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.284 (Depositor) 
• R-Value Work: 
  0.223 (Depositor) 

Literature

Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold

Zhou, C.-Z., Meyer, P., Quevillon-Cheruel, S., Li de La Sierra-Gallay, I., Collinet, B., Graille, M., Blondeau, K., Leulliot, N., Sorel, I., Poupon, A., Janin, J., Van Tilbeurgh, H.

(2005) Protein Sci 14: 209-215

• PubMed: 15608122 
• DOI: https://doi.org/10.1110/ps.041121305
• Primary Citation Related Structures: 
  1XE7, 1XE8


• PubMed Abstract: 
  

  We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 A. The protein has no close homologs and its molecular and cellular functions are unknown. The structure of the protein is a jelly-roll fold consisting of ten beta-strands organized in two parallel packed beta-sheets. The protein has strong structural resemblance to the plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) but also to some plant and bacterial enzymes (epimerase, germin). The protein forms homodimers in the crystal, confirming measurements of its molecular mass in solution. Two monomers have their beta-sheet packed together to form the dimer. The presence of a hydrophobic ligand in a well conserved pocket inside the barrel and local sequence similarity with bacterial epimerases may suggest a biochemical function for this protein.

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Organizational Affiliation: 
• Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8619, Université Paris-Sud, 91405 Orsay, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.13 kDa 
• Atom Count: 4,771 
• Modeled Residue Count: 570 
• Deposited Residue Count: 609 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region	A, B, C	203	Saccharomyces cerevisiae	Mutation(s): 3  Gene Names: YML079w
UniProt
Find proteins for Q03629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03629  Go to UniProtKB:  Q03629

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ADE	D [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
GOL	F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.284 (Depositor) 
• R-Value Work:  0.223 (Depositor) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.97	α = 90
b = 207.97	β = 90
c = 207.97	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Zhou, C.-Z., Meyer, P., Quevillon-Cheruel, S., Li de La Sierra-Gallay, I., Collinet, B., Graille, M., Leulliot, N., Sorel, I., Janin, J., Van Tilbeurgh, H.

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary