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 
  • R-Value Observed: 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 54: 776

  • DOI: 10.1002/prot.10596
  • Primary Citation of Related Structures:  
    1ODF

  • 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 feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGIONA290Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7
UniProt
Find proteins for P42938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42938 
Go to UniProtKB:  P42938
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42938
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.85α = 90
b = 64.85β = 90
c = 140.13γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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