1ODF

Structure of YGR205w protein.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structure of the Ygr205W Protein from Saccharomyces Cerevisiae: Close Structural Resemblance to E.Coli Pantothenate Kinase

Li De La Sierra-Gallay, I., Collinet, B., Graille, M., Quevillon-Cheruel, S., Liger, D., Minard, P., Blondeau, K., Henckes, G., Aufrere, R., Leulliot, N., Zhou, C.Z., Sorrel, I., Ferrer, J.L., Poupon, A., Janin, J., Van Tilbeurgh, H.

(2004) Proteins: Struct.,Funct., Genet. 54: 776

  • DOI: 10.1002/prot.10596

  • PubMed Abstract: 

    • The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence ...

    The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGION
A
290Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TDA10
EC: 2.7.-.-
Find proteins for P42938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P42938
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.850α = 90.00
b = 64.850β = 90.00
c = 140.130γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
SOLVE/RESOLVEphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance