PDBsum entry 1odf

Yeast protein

PDB id: 1odf

Contents

Protein chain

280 a.a. *

Ligands

SO4 ×2

GOL ×3

Waters ×74

* Residue conservation analysis

PDB id:

1odf

Name:

Yeast protein

Title:

Structure of ygr205w protein.

Structure:

Hypothetical 33.3 kda protein in ade3-ser2 intergenic region. Chain: a. Synonym: ygr205w. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: cloned gene

Resolution:

2.25Å R-factor: 0.206 R-free: 0.260

Authors:

I.Li De La Sierra-Gallay,H.Van Tilbeurgh

Key ref:

I.L.de La Sierra-Gallay et al. (2004). Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase. Proteins, 54, 776-783. PubMed id: 14997573 DOI: 10.1002/prot.10596

Date:

19-Feb-03 Release date: 12-Dec-03

Protein chain

P42938  (TDA10_YEAST) -  Probable ATP-dependent kinase TDA10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 290 a.a.

Struc: 280 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.-.-

DOI no: 10.1002/prot.10596

Proteins 54:776-783 (2004)

PubMed id: 14997573

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.

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

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. 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.

Selected figure(s)

Figure 1.
Figure 1. a: Stereo view of the 2Fo-Fc difference electron density map around the region of the P-loop, contoured at 2 . Clear residual electron density present in front of the P-loop was interpreted as a bound SO4-ion (ball and stick, Sulphur: green, Oxygen: red). b: Ball and stick representation of the SO[4]-ion bound to the P-loop. c: Ball and stick representation of the SO[4]-ion bound at the opposite site of the P-loop in the putative phosphate accepting substrate binding groove.

Figure 5.
Figure 5. The YGR255w and the pantothenate kinase Ca traces are in green and brown respectively. The YGR255w and pantothenate kinase P-loops are in yellow and orange, respectively. The YGR255w residues are represented as sticks and labelled in bold, those of pantothenate kinase are depicted in ball and sticks and labelled in italics. The Mg^2+ ion bound the AMPPNP is in cyan.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 776-783) copyright 2004.

Figures were selected by an automated process.