Evolution and classification of P-loop kinases and related proteins

Journal of Molecular Biology

Volumn 333, Issue 4, 2003, Pages 781-815

  Leipe, Detlef D ^a   Koonin, Eugene V ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

LUCA; Molecular evolution; P loop kinase

Indexed keywords

ADENOSINE 5' PHOSPHOSULFATE; ADENOSINE TRIPHOSPHATASE; AMIDE; DIHYDROFOLATE REDUCTASE; GUANOSINE TRIPHOSPHATASE; LIGASE; NUCLEOSIDE MONOPHOSPHATE KINASE; NUCLEOTIDE; PHOSPHOTRANSFERASE; POLYNUCLEOTIDE; PYRIMIDINE; SUGAR; SULFOTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CHEMICAL BOND; COENZYME; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME PHOSPHORYLATION; ENZYME SPECIFICITY; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN STRUCTURE; STANDARDIZATION;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0142011067     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.08.040     Document Type: Article

References (180)

1. Vetter I.R., Wittinghofer A. Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer. Quart. Rev. Biophys. 32:1999;1-56.
2. Koonin E.V., Wolf Y.I., Aravind L. Protein fold recognition using sequence profiles and its application in structural genomics. Advan. Protein Chem. 54:2000;245-275.
3. Doolittle R.F., Feng D.-F., Tsang S., Cho G., Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 271:1996;470-477.
4. Miyamoto M.M., Fitch W.M. Constraints on protein evolution and the age of the eubacteria/eukaryote split. Syst. Biol. 45:1996;568-575.
5. Leipe D.D., Wolf Y.I., Koonin E.V., Aravind L. Classification and evolution of P-loop GTPases and Related ATPases. J. Mol. Biol. 317:2002;41-72.
6. Anantharaman V., Koonin E.V., Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucl. Acids Res. 30:2002;1427-1464.
7. Walker J.E., Saraste M., Runswick M.J., Gay N.J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:1982;945-951.
8. Bourne H.R., Sanders D.A., McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature. 349:1991;117-127.
9. Gorbalenya A.E., Koonin E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3:1993;419-429.
10. Neuwald A.F., Aravind L., Spouge J.L., Koonin E.V. AAA[plus ]: a class of chaperone-like ATPases associated with the assembly operation, and disassembly of protein complexes. Genome Res. 9:1999;27-43.
11. Leipe D.D., Aravind L., Grishin N.V., Koonin E.V. The Bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res. 10:2000;5-16.
12. Cheek S., Zhang H., Grishin N.V. Sequence and structure classification of kinases. J. Mol. Biol. 320:2002;855-881.
13. Thompson T.B., Thomas M.G., Escalante-Semerena J.C., Rayment I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 Å resolution. Biochemistry. 37:1998;7686-7695.
14. Kakuta Y., Pedersen L.G., Carter C.W., Negishi M., Pedersen L.C. Crystal structure of estrogen sulphotransferase. Nature Struct. Biol. 4:1997;904-908.
15. Schauder S., Nunn R.S., Lanz R., Erni B., Schirmer T. Crystal structure of the IIB subunit of a fructose permease (IIBLev) from Bacillus subtilis. J. Mol. Biol. 276:1998;591-602.
16. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
17. Teplyakov A., Obmolova G., Tordova M., Thanki N., Bonander N., Eisenstein E., et al. Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis. Proteins: Struct. Funct. Genet. 48:2002;220-226.
18. Story R.M., Steitz T.A. Structure of the recA protein-ADP complex. Nature. 355:1992;374-376. see comments.
19. Campbell M.J., Davis R.W. On the in vivo function of the RecA ATPase. J. Mol. Biol. 286:1999;437-445.
20. Subramanya H.S., Bird L.E., Brannigan J.A., Wigley D.B. Crystal structure of a DExx box DNA helicase. Nature. 384:1996;379-383. See comments.
21. Hung L.W., Wang I.X., Nikaido K., Liu P.Q., Ames G.F., Kim S.H. Crystal structure of the ATP-binding subunit of an ABC transporter. Nature. 396:1998;703-707.
22. Herbig U., Marlar C.A., Fanning E. The Cdc6 nucleotide-binding site regulates its activity in DNA replication in human cells. Mol. Biol. Cell. 10:1999;2631-2645.
23. Sawaya M.R., Guo S., Tabor S., Richardson C.C., Ellenberger T. Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7. Cell. 99:1999;167-177.
24. Schulz G.E., Muller C.W., Diederichs K. Induced-fit movements in adenylate kinases. J. Mol. Biol. 213:1990;627-630.
25. Abele U., Schulz G.E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 4:1995;1262-1271.
26. Muller C.W., Schulz G.E. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state. J. Mol. Biol. 224:1992;159-177.
27. Ostermann N., Schlichting I., Brundiers R., Konrad M., Reinstein J., Veit T., et al. Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate. Struct. Fold. Des. 8:2000;629-642.
28. Vonrhein C., Bonisch H., Schafer G., Schulz G.E. The structure of a trimeric archaeal adenylate kinase. J. Mol. Biol. 282:1998;167-179.
29. Krell T., Coggins J.R., Lapthorn A.J. The three-dimensional structure of shikimate kinase. J. Mol. Biol. 278:1998;983-997.
30. Kraft L., Sprenger G.A., Lindqvist Y. Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography. J. Mol. Biol. 318:2002;1057-1069.
31. Obmolova G., Teplyakov A., Bonander N., Eisenstein E., Howard A.J., Gilliland G.L. Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae. J. Struct. Biol. 136:2001;119-125.
32. Hasemann C.A., Istvan E.S., Uyeda K., Deisenhofer J. The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Structure. 4:1996;1017-1029.
33. Kakuta Y., Pedersen L.G., Pedersen L.C., Negishi M. Conserved structural motifs in the sulfotransferase family. Trends Biochem. Sci. 23:1998;129-130.
34. Muller-Dieckmann H.J., Schulz G.E. The structure of uridylate kinase with its substrates, showing the transition state geometry. J. Mol. Biol. 236:1994;361-367.
35. 2+ at 2.2 Å: implications for water-mediated specificity. Biochemistry. 35:1996;9716-9727.
36. Yuen M.H., Wang X.L., Mizuguchi H., Uyeda K., Hasemann C.A. A switch in the kinase domain of rat testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. Biochemistry. 38:1999;12333-12342.
37. Schlichting I., Reinstein J. Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Biochemistry. 36:1997;9290-9296.
38. Yun M., Park C.G., Kim J.Y., Rock C.O., Jackowski S., Park H.W. Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J. Biol. Chem. 275:2000;28093-28099.
39. Stehle T., Schulz G.E. Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 Å resolution. J. Mol. Biol. 224:1992;1127-1141.
40. Bertrand T., Briozzo P., Assairi L., Ofiteru A., Bucurenci N., Munier-Lehmann H., et al. Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme. J. Mol. Biol. 315:2002;1099-1110.
41. Lavie A., Vetter I.R., Konrad M., Goody R.S., Reinstein J., Schlichting I. Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation. Nature Struct. Biol. 4:1997;601-604.
42. Lavie A., Konrad M., Brundiers R., Goody R.S., Schlichting I., Reinstein J. Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5′-adenosyl) P5-(5′-thymidyl) pentaphosphate (TP5A) at 2.0 Å resolution: implications for catalysis and AZT activation. Biochemistry. 37:1998;3677-3686.
43. Runquist J.A., Harrison D.H., Miziorko H.M. Rhodobacter sphaeroides phosphoribulokinase: identification of lysine-165 as a catalytic residue and evaluation of the contributions of invariant basic amino acids to ribulose 5-phosphate binding. Biochemistry. 38:1999;13999-14005.
44. Harrison D.H., Runquist J.A., Holub A., Miziorko H.M. The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase. Biochemistry. 37:1998;5074-5085.
45. Izard T., Ellis J. The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism. EMBO J. 19:2000;2690-2700.
46. Negishi M., Pedersen L.G., Petrotchenko E., Shevtsov S., Gorokhov A., Kakuta Y., Pedersen L.C. Structure and function of sulfotransferases. Arch. Biochem. Biophys. 390:2001;149-157.
47. Wang L.K., Lima C.D., Shuman S. Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme. EMBO J. 21:2002;3873-3880.
48. Uyeda K., Wang X.L., Mizuguchi H., Li Y., Nguyen C., Hasemann C.A. The active sites of fructose 6-phosphate,2-kinase: fructose-2,6-bisphosphatase from rat testis. Roles of Asp-128, Thr-52, Thr-130, Asn-73, and Tyr-197. J. Biol. Chem. 272:1997;7867-7872.
49. Wiesmuller L., Noegel A.A., Barzu O., Gerisch G., Schleicher M. cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli. J. Biol. Chem. 265:1990;6339-6345.
50. Schricker R., Magdolen V., Kaniak A., Wolf K., Bandlow W. The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase. Gene. 122:1992;111-118.
51. Muller-Dieckmann H.J., Schulz G.E. Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J. Mol. Biol. 246:1995;522-530.
52. Silva E., Ullu E., Kobayashi R., Tschudi C. Trypanosome capping enzymes display a novel two-domain structure. Mol. Cell. Biol. 18:1998;4612-4619.
53. Shuman S. Structure, mechanism, and evolution of the mRNA capping apparatus. Prog. Nucl. Acid Res. Mol. Biol. 66:2001;1-40.
54. Woods D.F., Bryant P.J. The discs-large tumor suppressor gene of Drosophila encodes a guanylate kinase homolog localized at septate junctions. Cell. 66:1991;451-464.
55. Koonin E.V., Woods D.F., Bryant P.J. dlg-R proteins: modified guanylate kinases. Nature Genet. 2:1992;256-257.
56. Anderson J.M. Cell signalling: MAGUK magic. Curr. Biol. 6:1996;382-384.
57. Kistner U., Garner C.C., Linial M. Nucleotide binding by the synapse associated protein SAP90. FEBS Letters. 359:1995;159-163.
58. Li Y., Spangenberg O., Paarmann I., Konrad M., Lavie A. Structural basis for nucleotide-dependent regulation of membrane-associated guanylate kinase-like domains. J. Biol. Chem. 277:2002;4159-4165.
59. Kim S.K. Tight junctions, membrane-associated guanylate kinases and cell signaling. Curr. Opin. Cell Biol. 7:1995;641-649.
60. McMahon L., Legouis R., Vonesch J.L., Labouesse M. Assembly of C. elegans apical junctions involves positioning and compaction by LET-413 and protein aggregation by the MAGUK protein DLG-1. J. Cell. Sci. 114:2001;2265-2277.
61. Bossinger O., Klebes A., Segbert C., Theres C., Knust E. Zonula adherens formation in Caenorhabditis elegans requires dlg-1, the homologue of the Drosophila gene discs large. Dev. Biol. 230:2001;29-42.
62. Metcalf W.W., Wanner B.L. Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements. J. Bacteriol. 175:1993;3430-3442.
63. Ropp P.A., Traut T.W. Cloning and expression of a cDNA encoding uridine kinase from mouse brain. Arch. Biochem. Biophys. 336:1996;105-112.
64. Van Rompay A.R., Norda A., Linden K., Johansson M., Karlsson A. Phosphorylation of uridine and cytidine nucleoside analogs by two human uridine-cytidine kinases. Mol. Pharmacol. 59:2001;1181-1186.
65. Calder R.B., Williams R.S., Ramaswamy G., Rock C.O., Campbell E., Unkles S.E., et al. Cloning and characterization of a eukaryotic pantothenate kinase gene (panK) from Aspergillus nidulans. J. Biol. Chem. 274:1999;2014-2020.
66. Lambert A., Osteras M., Mandon K., Poggi M.C., Le Rudulier D. Fructose uptake in Sinorhizobium meliloti is mediated by a high-affinity ATP-binding cassette transport system. J. Bacteriol. 183:2001;4709-4717.
67. 2 fixation and the evolution of autotrophy. Int. Microbiol. 2:1999;3-10.
68. Lehmacher A., Vogt A.B., Hensel R. Biosynthesis of cyclic 2,3-diphosphoglycerate. Isolation and characterization of 2-phosphoglycerate kinase and cyclic 2,3-diphosphoglycerate synthetase from Methanothermus fervidus. FEBS Letters. 272:1990;94-98.
69. Lehmacher A., Hensel R. Cloning, sequencing and expression of the gene encoding 2-phosphoglycerate kinase from Methanothermus fervidus. Mol. Gen. Genet. 242:1994;163-168.
70. Aravind L., Wolf Y.I., Koonin E.V. The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain. J. Mol. Microbiol. Biotechnol. 2:2000;191-194.
71. Lacher K., Schafer G. Archaebacterial adenylate kinase from the thermoacidophile Sulfolobus acidocaldarius: purification, characterization, and partial sequence. Arch. Biochem. Biophys. 302:1993;391-397.
72. Juhnke H., Charizanis C., Latifi F., Krems B., Entian K.D. The essential protein fap7 is involved in the oxidative stress response of Saccharomyces cerevisiae. Mol. Microbiol. 35:2000;936-948.
73. Bucurenci N., Sakamoto H., Briozzo P., Palibroda N., Serina L., Sarfati R.S., et al. CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases. J. Biol. Chem. 271:1996;2856-2862.
74. Briozzo P., Golinelli-Pimpaneau B., Gilles A.M., Gaucher J.F., Burlacu-Miron S., Sakamoto H., et al. Structures of Escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity. Structure. 6:1998;1517-1527.
75. Koonin E.V., Wolf Y.I., Aravind L. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11:2001;240-252.
76. Lavie A., Ostermann N., Brundiers R., Goody R.S., Reinstein J., Konrad M., Schlichting I. Structural basis for efficient phosphorylation of 3′-azidothymidine monophosphate by Escherichia coli thymidylate kinase. Proc. Natl Acad. Sci. USA. 95:1998;14045-14050.
77. Ma G.T., Hong Y.S., Ives D.H. Cloning and expression of the heterodimeric deoxyguanosine kinase/deoxyadenosine kinase of Lactobacillus acidophilus R-26. J. Biol. Chem. 270:1995;6595-6601.
78. Johansson M., Karlsson A. Cloning and expression of human deoxyguanosine kinase cDNA. Proc. Natl Acad. Sci. USA. 93:1996;7258-7262.
79. Koonin E.V., Senkevich T.G. Fowlpox virus encodes a protein related to human deoxycytidine kinase: further evidence for independent acquisition of genes for enzymes of nucleotide metabolism by different viruses. Virus Genes. 7:1993;289-295.
80. Loeffen J.L., Triepels R.H., van den Heuvel L.P., Schuelke M., Buskens C.A., Smeets R.J., et al. cDNA of eight nuclear encoded subunits of NADH:ubiquinone oxidoreductase: human complex I cDNA characterization completed. Biochem. Biophys. Res. Commun. 253:1998;415-422.
81. Wild K., Bohner T., Aubry A., Folkers G., Schulz G.E. The three-dimensional structure of thymidine kinase from herpes simplex virus type 1. FEBS Letters. 368:1995;289-292.
82. Wild K., Bohner T., Folkers G., Schulz G.E. The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue. Protein Sci. 6:1997;2097-2106.
83. Bork P., Holm L., Koonin E.V., Sander C. The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction. Proteins: Struct. Funct. Genet. 22:1995;259-266.
84. Singh S.K., Kurnasov O.V., Chen B., Robinson H., Grishin N.V., Osterman A.L., Zhang H. Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities. J. Biol. Chem. 277:2002;33291-33299.
85. Kelley L.A., MacCallum R.M., Sternberg M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299:2000;499-520.
86. Zhang H., Ishige K., Kornberg A. A polyphosphate kinase (PPK2) widely conserved in bacteria. Proc. Natl Acad. Sci. USA. 99:2002;16678-16683.
87. Ishige K., Zhang H., Kornberg A. Polyphosphate kinase (PPK2), a potent, polyphosphate-driven generator of GTP. Proc. Natl Acad. Sci. USA. 99:2002;16684-16688.
88. Teplyakov A., Sebastiao P., Obmolova G., Perrakis A., Brush G.S., Bessman M.J., Wilson K.S. Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. EMBO J. 15:1996;3487-3497.
89. Duckworth D.H., Bessman M.J. The enzymology of virus-infected bacteria. X. A biochemical-genetic study of the deoxynucleotide kinase induced by wild type and amber mutants of phage T4. J. Biol. Chem. 242:1967;2877-2885.
90. Olivier L.M., Chambliss K.L., Gibson K.M., Krisans S.K. Characterization of phosphomevalonate kinase: chromosomal localization, regulation, and subcellular targeting. J. Lipid Res. 40:1999;672-679.
91. Huang K.X., Scott A.I., Bennett G.N. Overexpression, purification, and characterization of the thermostable mevalonate kinase from Methanococcus jannaschii. Protein Exptl Purif. 17:1999;33-40.
92. Houten S.M., Waterham H.R. Nonorthologous gene displacement of phosphomevalonate kinase. Mol. Genet. Metab. 72:2001;273-276.
93. Zhou T., Daugherty M., Grishin N.V., Osterman A.L., Zhang H. Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Struct. Fold. Des. 8:2000;1247-1257.
94. Schmid J., Schaller A., Leibinger U., Boll W., Amrhein N. The in vitro synthesized tomato shikimate kinase precursor is enzymatically active and is imported and processed to the mature enzyme by chloroplasts. Plant J. 2:1992;375-383.
95. Bork P., Sander C., Valencia A. Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Protein Sci. 2:1993;31-40.
96. Daugherty M., Vonstein V., Overbeek R., Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183:2001;292-300.
97. Tong S., Porco A., Isturiz T., Conway T. Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism. J. Bacteriol. 178:1996;3260-3269.
98. Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T. Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli. J. Bacteriol. 180:1998;3704-3710.
99. Izu H., Adachi O., Yamada M. Purification and characterization of the Escherichia coli thermoresistant glucokinase encoded by the gntK gene. FEBS Letters. 394:1996;14-16.
100. Mishra P., Park P.K., Drueckhammer D.G. Identification of yacE (coaE) as the structural gene for dephosphocoenzyme A kinase in Escherichia coli K-12. J. Bacteriol. 183:2001;2774-2778.
101. Daugherty M., Polanuyer B., Farrell M., Scholle M., Lykidis A., de Crecy-Lagard V., Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277:2002;21431-21439.
102. Aravind L., Anantharaman V., Koonin E.V. Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins: Struct. Funct. Genet. 48:2002;1-14.
103. Smith C.A., Rayment I. Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys. J. 70:1996;1590-1602.
104. MacRae I.J., Segel I.H., Fisher A.J. Crystal structure of adenosine 5′-phosphosulfate kinase from Penicillium chrysogenum. Biochemistry. 39:2000;1613-1621.
105. Rosenthal E., Leustek T. A multifunctional Urechis caupo protein, PAPS synthetase, has both ATP sulfurylase and APS kinase activities. Gene. 165:1995;243-248.
106. Venkatachalam K.V., Akita H., Strott C.A. Molecular cloning, expression, and characterization of human bifunctional 3′-phosphoadenosine 5′-phosphosulfate synthase and its functional domains. J. Biol. Chem. 273:1998;19311-19320.
107. Cervantes E., Sharma S.B., Maillet F., Vasse J., Truchet G., Rosenberg C. The Rhizobium meliloti host range nodQ gene encodes a protein which shares homology with translation elongation and initiation factors. Mol. Microbiol. 3:1989;745-755.
108. Schwedock J.S., Liu C., Leyh T.S., Long S.R. Rhizobium meliloti NodP and NodQ form a multifunctional sulfate-activating complex requiring GTP for activity. J. Bacteriol. 176:1994;7055-7064.
109. Abola A.P., Willits M.G., Wang R.C., Long S.R. Reduction of adenosine-5′-phosphosulfate instead of 3′-phosphoadenosine-5′ -phosphosulfate in cysteine biosynthesis by Rhizobium meliloti and other members of the family Rhizobiaceae. J. Bacteriol. 181:1999;5280-5287.
110. Aravind L., Koonin E.V. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucl. Acids Res. 26:1998;3746-3752.
111. Aravind L., Galperin M.Y., Koonin E.V. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem. Sci. 23:1998;127-129.
112. Aravind L., Koonin E.V., The H.D. domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23:1998;469-472.
113. Mazumder R., Lakshminarayan M.I., Vasudevaan S., Aravind L. Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nucl. Acids Res. 30:2002;1-15.
114. Jilani A., Ramotar D., Slack C., Ong C., Yang X.M., Scherer S.W., Lasko D.D. Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3′-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage. J. Biol. Chem. 274:1999;24176-24186.
115. Karimi-Busheri F., Daly G., Robins P., Canas B., Pappin D.J., Sgouros J., et al. Molecular characterization of a human DNA kinase. J. Biol. Chem. 274:1999;24187-24194.
116. Meijer M., Karimi-Busheri F., Huang T.Y., Weinfeld M., Young D. Pnk1, a DNA kinase/phosphatase required for normal response to DNA damage by gamma-radiation or camptothecin in Schizosaccharomyces pombe. J. Biol. Chem. 277:2002;4050-4055.
117. Amitsur M., Levitz R., Kaufmann G. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 6:1987;2499-2503.
118. Betti M., Petrucco S., Bolchi A., Dieci G., Ottonello S. A plant 3′-phosphoesterase involved in the repair of DNA strand breaks generated by oxidative damage. J. Biol. Chem. 276:2001;18038-18045.
119. Romig H., Fackelmayer F.O., Renz A., Ramsperger U., Richter A. Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J. 11:1992;3431-3440.
120. Fackelmayer F.O., Dahm K., Renz A., Ramsperger U., Richter A. Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur. J. Biochem. 221:1994;749-757.
121. Gohring F., Fackelmayer F.O. The scaffold/matrix attachment region binding protein hnRNP-U (SAF-A) is directly bound to chromosomal DNA in vivo: a chemical cross-linking study. Biochemistry. 36:1997;8276-8283.
122. Aravind L., Koonin E.V. SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem. Sci. 25:2000;112-114.
123. Aravind L., Koonin E.V. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res. 11:2001;1365-1374.
124. Xu Q., Teplow D., Lee T.D., Abelson J. Domain structure in yeast tRNA ligase. Biochemistry. 29:1990;6132-6138.
125. Phizicky E.M., Consaul S.A., Nehrke K.W., Abelson J. Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates. J. Biol. Chem. 267:1992;4577-4582.
126. Koonin E.V., Gorbalenya A.E. Related domains in yeast tRNA ligase, bacteriophage T4 polynucleotide kinase and RNA ligase, and mammalian myelin 2′,3′-cyclic nucleotide phosphohydrolase revealed by amino acid sequence comparison. FEBS Letters. 268:1990;231-234.
127. Zhang C.C., Friry A., Peng L. Molecular and genetic analysis of two closely linked genes that encode, respectively, a protein phosphatase 1/2A/2B homolog and a protein kinase homolog in the cyanobacterium Anabaena sp. strain PCC 7120. J. Bacteriol. 180:1998;2616-2622.
128. Thompson R.J. 2′,3′-cyclic nucleotide-3′ -phosphohydrolase and signal transduction in central nervous system myelin. Biochem. Soc. Trans. 20:1992;621-626.
129. Sherrington R., Rogaev E.I., Liang Y., Rogaeva E.A., Levesque G., Ikeda M., Chi H., et al. Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature. 375:1995;754-760.
130. Misawa K., Nosaka T., Morita S., Kaneko A., Nakahata T., Asano S., Kitamura T. A method to identify cDNAs based on localization of green fluorescent protein fusion products. Proc. Natl Acad. Sci. USA. 97:2000;3062-3066.
131. Murillas R., Simms K.S., Hatakeyama S., Weissman A.M., Kuehn M.R. Identification of developmentally expressed proteins that functionally interact with Nedd4 ubiquitin ligase. J. Biol. Chem. 277:2002;2897-2907.
132. Moreira D., Philippe H. Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family. Trends Biochem. Sci. 24:1999;298-300.
133. Butler A.R., White J.H., Folawiyo Y., Edlin A., Gardiner D., Stark M.J. Two Saccharomyces cerevisiae genes which control sensitivity to G1 arrest induced by Kluyveromyces lactis toxin. Mol. Cell. Biol. 14:1994;6306-6316.
134. Bancroft I., Jones J.D., Dean C. Heterologous transposon tagging of the DRL1 locus in Arabidopsis. Plant Cell. 5:1993;631-638.
135. Tillett D., Dittmann E., Erhard M., von Dohren H., Borner T., Neilan B.A. Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptide-polyketide synthetase system. Chem. Biol. 7:2000;753-764.
136. Barrasa M.I., Tercero J.A., Jimenez A. The aminonucleoside antibiotic A201A is inactivated by a phosphotransferase activity from Streptomyces capreolus NRRL 3817, the producing organism. Isolation and molecular characterization of the relevant encoding gene and its DNA flanking regions. Eur. J. Biochem. 245:1997;54-63.
137. Peschke U., Schmidt H., Zhang H.Z., Piepersberg W. Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. Mol. Microbiol. 16:1995;1137-1156.
138. Mosher R.H., Camp D.J., Yang K., Brown M.P., Shaw W.V., Vining L.C. Inactivation of chloramphenicol by O-phosphorylation. A novel resistance mechanism in Streptomyces venezuelae ISP5230, a chloramphenicol producer. J. Biol. Chem. 270:1995;27000-27006.
139. Aboulmagd E., Oppermann-Sanio F.B., Steinbuchel A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174:2000;297-306.
140. Krehenbrink M., Oppermann-Sanio F.B., Steinbuchel A. Evaluation of non-cyanobacterial genome sequences for occurrence of genes encoding proteins homologous to cyanophycin synthetase and cloning of an active cyanophycin synthetase from Acinetobacter sp. strain DSM 587. Arch. Microbiol. 177:2002;371-380.
141. Eveland S.S., Pompliano D.L., Anderson M.S. Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-gamma-glutamate ligases: identification of a ligase superfamily. Biochemistry. 36:1997;6223-6229.
142. Sheng Y., Sun X., Shen Y., Bognar A.L., Baker E.N., Smith C.A. Structural and functional similarities in the ADP-forming amide bond ligase superfamily: implications for a substrate-induced conformational change in folylpolyglutamate synthetase. J. Mol. Biol. 302:2000;427-440.
143. Aboulmagd E., Oppermann-Sanio F.B., Steinbuchel A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67:2001;2176-2182.
144. Bertrand J.A., Auger G., Fanchon E., Martin L., Blanot D., van Heijenoort J., Dideberg O. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. EMBO J. 16:1997;3416-3425.
145. Sun X., Bognar A.L., Baker E.N., Smith C.A. Structural homologies with ATP- and folate-binding enzymes in the crystal structure of folylpolyglutamate synthetase. Proc. Natl Acad. Sci. USA. 95:1998;6647-6652.
146. Bertrand J.A., Auger G., Martin L., Fanchon E., Blanot D., Le Beller D., et al. Determination of the MurD mechanism through crystallographic analysis of enzyme complexes. J. Mol. Biol. 289:1999;579-590.
147. Pakhomova S., Kobayashi M., Buck J., Newcomer M.E. A helical lid converts a sulfotransferase to a dehydratase. Nature Struct. Biol. 8:2001;447-451.
148. 2 fixation on phosphoenolpyruvate. Boyer P.D. The Enzymes. The Enzymes. vol. 6:1972;117-168 Academic Press, New York.
149. Kravanja M., Engelmann R., Dossonnet V., Bluggel M., Meyer H.E., Frank R., et al. The hprK gene of Enterococcus faecalis encodes a novel bifunctional enzyme: the HPr kinase/phosphatase. Mol. Microbiol. 31:1999;59-66.
150. Matte A., Goldie H., Sweet R.M., Delbaere L.T. Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: a new structural family with the P-loop nucleoside triphosphate hydrolase fold. J. Mol. Biol. 256:1996;126-143.
151. Fieulaine S., Morera S., Poncet S., Monedero V., Gueguen-Chaignon V., Galinier A., et al. X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain. EMBO J. 20:2001;3917-3927.
152. Sudom A.M., Prasad L., Goldie H., Delbaere L.T. The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3). J. Mol. Biol. 314:2001;83-92.
153. Matte A., Tari L.W., Goldie H., Delbaere L.T. Structure and mechanism of phosphoenolpyruvate carboxykinase. J. Biol. Chem. 272:1997;8105-8108.
154. Koonin E.V., Makarova K.S., Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55:2001;709-742.
155. Blakley R.L. Eukaryotic dihydrofolate reductase. Advan. Enzymol. Relat. Areas Mol. Biol. 70:1995;23-102.
156. Richter G., Fischer M., Krieger C., Eberhardt S., Luttgen H., Gerstenschlager I., Bacher A. Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis. J. Bacteriol. 179:1997;2022-2028.
157. Li R., Sirawaraporn R., Chitnumsub P., Sirawaraporn W., Wooden J., Athappilly F., et al. Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. J. Mol. Biol. 295:2000;307-323.
158. +. Biochemistry. 38:1999;4303-4312.
159. Nikaido H., Saier M.H. Jr. Transport proteins in bacteria: common themes in their design. Science. 258:1992;936-942.
160. Saier M.H. Jr, Reizer J. The bacterial phosphotransferase system: new frontiers 30 years later. Mol. Microbiol. 13:1994;755-764.
161. Makarova K.S., Aravind L., Wolf Y.I., Tatusov R.L., Minton K.W., Koonin E.V., Daly M.J. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65:2001;44-79.
162. Doolittle W.F. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14:1998;307-311.
163. Iyer L.M., Aravind L., Koonin E.V. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75:2001;11720-11734.
164. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
165. Altschul S.F., Koonin E.V. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci. 23:1998;444-447.
166. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., Gibson T.J. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23:1998;403-405.
167. Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:2000;205-217.
168. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl. Acids Res. 29:2001;22-28.
169. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:1992;275-282.
170. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. 2002;Sinauer Associates, Sunderland, MA.
171. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea. Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA. 87:1990;4576-4579.
172. Gibrat J.F., Madej T., Bryant S.H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6:1996;377-385.
173. Madej T., Gibrat J.F., Bryant S.H. Threading a database of protein cores. Proteins: Struct. Funct. Genet. 23:1995;356-369.
174. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-603.
175. Shakhnovich B.E., Dokholyan N.V., DeLisi C., Shakhnovich E.I. Functional fingerprints of folds: evidence for correlated structure-function evolution. J. Mol. Biol. 326:2003;1-9.
176. Rost B. PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol. 266:1996;525-539.
177. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18:1997;2714-2723.
178. Barton G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6:1993;37-40.
179. Wang Y., Geer L.Y., Chappey C., Kans J.A., Bryant S.H. Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci. 25:2000;300-302.
180. +)-release channels). Trends Biochem. Sci. 22:1997;193-194.