Crystal Structure of the YGR205w Protein from Saccharomyces cerevisiae: Close Structural Resemblance to E. coli Pantothenate Kinase

Proteins: Structure, Function and Genetics

Volumn 54, Issue 4, 2004, Pages 776-783

  De La Sierra Gallay, Ines Li ^a   Collinet, Bruno ^b   Graille, Marc ^a   Quevillon Cheruel, Sophie ^b   Liger, Dominique ^b   Minard, Philippe ^b   Blondeau, Karine ^c   Henckes, Gilles ^c   Aufrère, Robert ^c   Leulliot, Nicolas ^b   Zhou, Cong Zhao ^b   Sorel, Isabelle ^b   Ferrer, Jean Luc ^d   Poupon, Anne ^a   Janin, Joël ^a   Van Tilbeurgh, Herman ^b  

^a LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^b INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^c UNIVERSITÉ PARIS SACLAY   (France)

^d INSTITUT DE BIOLOGIE STRUCTURALE   (France)

Author keywords

Crystal structure; Kinase; Mononucleotide binding fold; Nucleotide; P loop; Structural genomics; Yeast; YGR205w

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; AMINO ACID; BACTERIAL ENZYME; FUNGAL PROTEIN; METHIONINE; NUCLEOTIDE BINDING PROTEIN; PANTOTHENATE KINASE; PHOSPHORIBULOKINASE; SELENIUM; SULFATE; UNCLASSIFIED DRUG; YGR205W PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIFFRACTION; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; FUNGAL GENE; GENOME ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TARGETING; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; STRUCTURAL GENE; STRUCTURE ANALYSIS;

SACCHAROMYCES CEREVISIAE;

EID: 10744232362     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10596     Document Type: Article

References (30)

1. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfeiffer F, Zollner A. Overview of the yeast genome. Nature 1997;387(6632 Suppl):7-65.
2. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002; 418 (6896):387-391.
3. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH. Functional discovery via a compendium of expression profiles. Cell 2000;102(1):109-126.
4. Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L, Heidtman M, Nelson FK, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder GS, Snyder M. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999;402(6760): 413-418.
5. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Davis RW, et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999;285(5429):901-906.
6. Brenner SE, Levitt M. Expectations from structural genomics. Protein Sci 2000;9(1):197-200.
7. Sali A. 100,000 protein structures for the biologist. Nat Struct Biol 1998;5 (12):1029-1032.
8. Hegyi H, Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 1999;288(1):147-164.
9. Vitkup D, Melamud E, Moult J, Sander C. Completeness in structural genomics. Nat Struct Biol 2001;8(6):559-566.
10. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci USA 1998;95(26):15189-15193.
11. Quevillon-Cheruel S, Collinet B, Zhou CZ, Minard P, Blondeau K, Henkes G, Aufrere R, Coutant J, Guittet E, Lewit-Bentley A, Leulliot N, Ascone I, Sorel I, Savarin P, De La Sierra Gallay IL, De La Torre F, Poupon A, Fourme R, Janin J, Van Tilbeurgh H. A structural genomics initiative on yeast proteins. J Synchrotron Radiat 2003;10(Pt 1):4-8.
12. Saraste M, Sibbald PR, Wittinghofer A. The P-loop-a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 1990;15(11):430-434.
13. Otwinowski Z, Minor W. Processing of X-ray diffraction data collection in oscillation mode. Methods Enzymol 1997;276:307-326.
14. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr Collaborative Computational Project 4 1994;50:760-763.
15. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54(Pt 5):905-921.
16. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1997;55:849-861.
17. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
18. Schulz GE. Binding of nucleotides by proteins. Curr Biol 1992;2: 61-67.
19. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-128.
20. Yun M, Park CG, Kim JY, Rock CO, Jackowski S, Park HW. Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J Biol Chem 2000;275(36): 28093-28099.
21. Harrison DH, Runquist JA, Holub A, Miziorko HM. The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase. Biochemistry 1998;37(15):5074-5085.
22. Hasemann CA, Istvan ES, Uyeda K, Deisenhofer J. The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Structure 1996;4(9):1017-1029.
23. Berry MB, Phillips NJ. Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Proteins 1998;32: 276-288.
24. Li de la Sierra I, Munier-Lehmann H, Gilles AM, Barzu O, Delarue M. X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution. J Mol Biol 2001;311(1):87-100.
25. Koteiche HA, Narasimhan C, Runquist JA, Miziorko HM. Utility of a novel spin-labeled nucleotide in investigation of the substrate and effector sites of phosphoribulokinase. Biochemistry 1995; 34(46):15068-15074.
26. Sekulic N, Shuvalova L, Spangenberg O, Konrad M, Lavie A. Structural characterization of the closed conformation of mouse guanylate kinase. J Biol Chem 2002;277(33):30236-30243.
27. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8(2):127-134.
28. Charlier HA, Jr., Runquist JA, Miziorko HM. Evidence supporting catalytic roles for aspartate residues in phosphoribulokinase. Biochemistry 1994;33 (31):9343-9350.
29. Runquist JA, Harrison DH, Miziorko HM. Functional evaluation of invariant arginines situated in the mobile lid domain of phosphoribulokinase. Biochemistry 1998;37(5):1221-1226.
30. Schulz GE. Induced-fit movements in adenylate kinases. Faraday Discuss 1992;93:85-93.