Classification and evolution of P-loop GTPases and related ATPases

Saraste, 1990, The P-loop – a common motif in ATP- and GTP-binding proteins, Trends Biochem. Sci., 15, 430, 10.1016/0968-0004(90)90281-F Gorbalenya, 1990, Superfamily of UvrA-related NTP-binding proteins. Implications for rational classification of recombination/repair systems, J. Mol. Biol., 213, 583, 10.1016/S0022-2836(05)80243-8 Milner-White, 1991, Evidence for an ancestral core structure in nucleotide-binding proteins with the type A motif, J. Mol. Biol., 221, 751, 10.1016/0022-2836(91)80170-Y Schulz, 1992, Binding of nucleotides by proteins, Curr. Opin. Struct. Biol., 2, 61, 10.1016/0959-440X(92)90178-A Schweins, 1994, GTP-binding proteins. Structures, interactions and relationships, Curr. Biol., 4, 547, 10.1016/S0960-9822(00)00122-6 Vetter, 1999, Nucleoside triphosphate-binding proteins, Quart. Rev. Biophys., 32, 1, 10.1017/S0033583599003480 Koonin, 2000, Protein fold recognition using sequence profiles and its application in structural genomics, Advan. Protein Chem., 54, 245, 10.1016/S0065-3233(00)54008-X Walker, 1982, 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, 945, 10.1002/j.1460-2075.1982.tb01276.x Bourne, 1991, The GTPase superfamily, Nature, 349, 117, 10.1038/349117a0 Gorbalenya, 1993, Helicases, Curr. Opin. Struct. Biol., 3, 419, 10.1016/S0959-440X(05)80116-2 Neuwald, 1999, AAA+, Genome Res., 9, 27, 10.1101/gr.9.1.27 Leipe, 2000, The bacterial replicative helicase DnaB evolved from a RecA duplication, Genome Res., 10, 5 Rodnina, 2000, GTPases mechanisms and functions of translation factors on the ribosome, Biol. Chem., 381, 377, 10.1515/BC.2000.050 Takai, 2001, Small GTP-binding proteins, Physiol. Rev., 81, 153, 10.1152/physrev.2001.81.1.153 Kabsch, 1977, Low resolution structure of partially trypsin-degraded polypeptide elongation factor, EF-Tu, from Escherichia coli, J. Mol. Biol., 117, 999, 10.1016/S0022-2836(77)80009-0 Halliday, 1983, Regional homology in GTP-binding proto-oncogene products and elongation factors, J. Cyclic Nucleotide Protein Phosphor. Res., 9, 435 Jurnak, 1985, Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins, Science, 230, 32, 10.1126/science.3898365 McCormick, 1985, A model for the tertiary structure of p21, the product of the ras oncogene, Science, 230, 78, 10.1126/science.3898366 Macara, 1996, The Ras superfamily of GTPases, FASEB J., 10, 625, 10.1096/fasebj.10.5.8621061 Garcia-Ranea, 1998, Distribution and functional diversification of the ras superfamily in Saccharomyces cerevisiae, FEBS Letters, 434, 219, 10.1016/S0014-5793(98)00967-3 Yu, 1995, Structure of guanine-nucleotide-exchange factor human Mss4 and identification of its Rab-interacting surface, Nature, 376, 788, 10.1038/376788a0 Barrett, 1997, The structure of the GTPase-activating domain from p50rhoGAP, Nature, 385, 458, 10.1038/385458a0 Nassar, 1998, Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP, Nature Struct. Biol., 5, 1047, 10.1038/4156 Zhu, 2001, A helical turn motif in Mss4 is a critical determinant of Rab binding and nucleotide release, Biochemistry, 40, 3027, 10.1021/bi002680o Trimble, 1999, Septins, J. Membr. Biol., 169, 75, 10.1007/s002329900519 Field, 1999, Septins, Trends Cell Biol., 9, 387, 10.1016/S0962-8924(99)01632-3 Hales, 1997, Developmentally regulated mitochondrial fusion mediated by a conserved, novel, predicted GTPase, Cell, 90, 121, 10.1016/S0092-8674(00)80319-0 Marks, 2001, GTPase activity of dynamin and resulting conformation change are essential for endocytosis, Nature, 410, 231, 10.1038/35065645 Czworkowski, 1994, The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution, EMBO J., 13, 3661, 10.1002/j.1460-2075.1994.tb06675.x Choi, 1998, Promotion of met-tRNAiMet binding to ribosomes by yIF2, a bacterial IF2 homolog in yeast, Science, 280, 1757, 10.1126/science.280.5370.1757 Chen, 1999, Crystal structure of ERA, Proc. Natl Acad. Sci. USA, 96, 8396, 10.1073/pnas.96.15.8396 Pestova, 2000, The joining of ribosomal subunits in eukaryotes requires eIF5B, Nature, 403, 332, 10.1038/35002118 Scott, 2000, The Bacillus subtilis GTP binding protein obg and regulators of the sigma(B) stress response transcription factor cofractionate with ribosomes, J. Bacteriol., 182, 2771, 10.1128/JB.182.10.2771-2777.2000 Freymann, 1999, Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP, Nature Struct. Biol., 6, 793, 10.1038/11572 Montoya, 2000, The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex, Struct. Fold. Des., 8, 515, 10.1016/S0969-2126(00)00131-3 Tatusov, 2000, The COG database, Nucl. Acids Res., 28, 33, 10.1093/nar/28.1.33 Mittenhuber, 2001, Comparative genomics of prokaryotic GTP-binding proteins (the Era, Obg, EngA, ThdF (TrmE), YchF and YihA families) and their relationship to eukaryotic GTP-binding proteins (the DRG, ARF, RAB, RAN, RAS and RHO families), J. Mol. Microbiol. Biotechnol., 3, 21 Caldon, 2001, Evolution of a molecular switch, Mol. Microbiol., 41, 289, 10.1046/j.1365-2958.2001.02536.x Smith, 1996, Active site comparisons highlight structural similarities between myosin and other P-loop proteins, Biophys. J., 70, 1590, 10.1016/S0006-3495(96)79745-X Kull, 1998, The case for a common ancestor, J. Muscle Res. Cell Motil., 19, 877, 10.1023/A:1005489907021 Harton, 1999, GTP binding by class II transactivator, Science, 285, 1402, 10.1126/science.285.5432.1402 Pieper, 1997, Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP, J. Mol. Biol., 272, 190, 10.1006/jmbi.1997.1228 Murzin, 1995, SCOP, J. Mol. Biol., 247, 536, 10.1006/jmbi.1995.0159 Lo Conte, 2000, SCOP, Nucl. Acids Res., 28, 257, 10.1093/nar/28.1.257 Orengo, 1997, CATH - a hierarchic classification of protein domain structures, Structure, 5, 1093, 10.1016/S0969-2126(97)00260-8 Orengo, 1999, From protein structure to function, Curr. Opin. Struct. Biol., 9, 374, 10.1016/S0959-440X(99)80051-7 Holm, 1998, Touring protein fold space with Dali/FSSP, Nucl. Acids Res., 26, 316, 10.1093/nar/26.1.316 Doolittle, 1998, Evolutionary anomalies among the aminoacyl-tRNA synthetases, Curr. Opin. Genet. Dev., 8, 630, 10.1016/S0959-437X(98)80030-0 Story, 1992, Structure of the recA protein-ADP complex, Nature, 355, 374, 10.1038/355374a0 Brosh, 1995, Mutations in motif II of Escherichia coli DNA helicase II render the enzyme nonfunctional in both mismatch repair and excision repair with differential effects on the unwinding reaction, J. Bacteriol., 177, 5612, 10.1128/jb.177.19.5612-5621.1995 Subramanya, 1996, Crystal structure of a DExx box DNA helicase, Nature, 384, 379, 10.1038/384379a0 Hung, 1998, Crystal structure of the ATP-binding subunit of an ABC transporter, Nature, 396, 703, 10.1038/25393 Campbell, 1999, On the in vivo function of the RecA ATPase, J. Mol. Biol., 286, 437, 10.1006/jmbi.1998.2457 Soultanas, 1999, DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase, J. Mol. Biol., 290, 137, 10.1006/jmbi.1999.2873 Perkins, 1998, Nucleotide-dependent prereplicative complex assembly by Cdc6p, a homolog of eukaryotic and prokaryotic clamp- loaders, Mol. Cell, 2, 23, 10.1016/S1097-2765(00)80110-0 Herbig, 1999, The Cdc6 nucleotide-binding site regulates its activity in DNA replication in human cells, Mol. Biol. Cell, 10, 2631, 10.1091/mbc.10.8.2631 Sondek, 1994, GTPase mechanism of Gproteins from the 1.7-Å crystal structure of transducin alpha-GDP-AIF-4, Nature, 372, 276, 10.1038/372276a0 Schweins, 1997, The role of the metal ion in the p21ras catalysed GTP-hydrolysis, J. Mol. Biol., 266, 847, 10.1006/jmbi.1996.0814 Coleman, 1994, Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis, Science, 265, 1405, 10.1126/science.8073283 Berchtold, 1993, Crystal structure of active elongation factor Tu reveals major domain rearrangements, Nature, 365, 126, 10.1038/365126a0 Zhang, 1998, Mutational analysis of the roles of residues in Escherichia coli elongation factor Ts in the interaction with elongation factor Tu, J. Biol. Chem., 273, 4556, 10.1074/jbc.273.8.4556 Forchhammer, 1989, Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein, Nature, 342, 453, 10.1038/342453a0 Kromayer, 1996, Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB, J. Mol. Biol., 262, 413, 10.1006/jmbi.1996.0525 Merrick, 1992, Mechanism and regulation of eukaryotic protein synthesis, Microbiol. Rev., 56, 291, 10.1128/MR.56.2.291-315.1992 Lee, 1999, Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2, Proc. Natl Acad. Sci. USA, 96, 4342, 10.1073/pnas.96.8.4342 Wallrapp, 1998, The product of the mammalian orthologue of the Saccharomyces cerevisiae HBS1 gene is phylogenetically related to eukaryotic release factor 3 (eRF3) but does not carry eRF3-like activity, FEBS Letters, 440, 387, 10.1016/S0014-5793(98)01492-6 Inagaki, 2000, Evolution of the eukaryotic translation termination system, Mol. Biol. Evol., 17, 882, 10.1093/oxfordjournals.molbev.a026368 Shoemaker, 2001, Evidence for extensive resistance gene transfer among bacteroides sand among bacteroides and other genera in the human colon, Appl. Environ. Microbiol., 67, 561, 10.1128/AEM.67.2.561-568.2001 Leyh, 1988, The sulfate activation locus of Escherichia coli K12, J. Biol. Chem., 263, 2409, 10.1016/S0021-9258(18)69222-1 Schwedock, 1990, ATP sulphurylase activity of the nodP and nodQ gene products of Rhizobium meliloti, Nature, 348, 644, 10.1038/348644a0 Keeling, 1995, Archaea, Proc. Natl Acad. Sci. USA, 92, 5761, 10.1073/pnas.92.13.5761 Keeling, 1998, Evolutionary relationship between translation initiation factor eIF-2gamma and selenocysteine-specific elongation factor SELB, J. Mol. Evol., 47, 649, 10.1007/PL00006422 Avarsson, 1995, Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation, J. Mol. Evol., 41, 1096 Rout, 2000, The yeast nuclear pore complex, J. Cell Biol., 148, 635, 10.1083/jcb.148.4.635 Casalone, 1999, Disruption and phenotypic analysis of six novel genes from chromosome IV of Saccharomyces cerevisiae reveal YDL060w as an essential gene for vegetative growth, Yeast, 15, 1691, 10.1002/(SICI)1097-0061(199911)15:15<1691::AID-YEA489>3.0.CO;2-0 Noble, 1993, The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain, Proc. Natl Acad. Sci. USA, 90, 10866, 10.1073/pnas.90.22.10866 Maddock, 1997, Identification of an essential Caulobacter crescentus gene encoding a member of the Obg family of GTP-binding proteins, J. Bacteriol., 179, 6426, 10.1128/jb.179.20.6426-6431.1997 Okamoto, 1997, Molecular cloning and characterization of the obg gene of Streptomyces griseus in relation to the onset of morphological differentiation, J. Bacteriol., 179, 170, 10.1128/jb.179.1.170-179.1997 Wolf, 1999, Evolution of aminoacyl-tRNA synthetases – analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events, Genome Res., 9, 689, 10.1101/gr.9.8.689 Park, 2001, A novel nucleolar G-protein conserved in eukaryotes, J. Cell Sci., 114, 173, 10.1242/jcs.114.1.173 Decoster, 1993, MSS1, a nuclear-encoded mitochondrial GTPase involved in the expression of COX1 subunit of cytochrome c oxidase, J. Mol. Biol., 232, 79, 10.1006/jmbi.1993.1371 Wolf, 2001, Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context, Genome Res., 11, 356, 10.1101/gr.GR-1619R Cabedo, 1999, The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties, EMBO J., 18, 7063, 10.1093/emboj/18.24.7063 Kammler, 1993, Characterization of the ferrous iron uptake system of Escherichia coli, J. Bacteriol., 175, 6212, 10.1128/jb.175.19.6212-6219.1993 Arigoni, 1998, A genome-based approach for the identification of essential bacterial genes, Nature Biotechnol., 16, 851, 10.1038/nbt0998-851 Dassain, 1999, A new essential gene of the ‘minimal genome’ affecting cell division, Biochimie, 81, 889, 10.1016/S0300-9084(99)00207-2 Zuber, 1997, A Francisella tularensis DNA clone complements Escherichia coli defective for the production of Era, an essential Ras-like GTP-binding protein, Gene, 189, 31, 10.1016/S0378-1119(96)00813-X Johnstone, 1999, The widely conserved Era G-protein contains an RNA-binding domain required for Era function in vivo, Mol. Microbiol., 33, 1118, 10.1046/j.1365-2958.1999.01553.x Gollop, 1991, A GTP-binding protein (Era) has an essential role in growth rate and cell cycle control in Escherichia coli, J. Bacteriol., 173, 2265, 10.1128/jb.173.7.2265-2270.1991 Britton, 1998, Cell cycle arrest in Era GTPase mutants, Mol. Microbiol., 27, 739, 10.1046/j.1365-2958.1998.00719.x Meier, 2000, Era GTPase of Escherichia coli, Microbiology, 146, 1071, 10.1099/00221287-146-5-1071 Mehr, 2000, A homologue of the recombination-dependent growth gene, rdgC, is involved in gonococcal pilin antigenic variation, Genetics, 154, 523, 10.1093/genetics/154.2.523 Neufeld, 1994, The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast putative bud neck filament proteins, Cell, 77, 371, 10.1016/0092-8674(94)90152-X Kartmann, 2001, Novel roles for mammalian septins, J. Cell Sci., 114, 839, 10.1242/jcs.114.5.839 Zhang, 1999, Phosphatidylinositol polyphosphate binding to the mammalian septin H5 is modulated by GTP, Curr. Biol., 9, 1458, 10.1016/S0960-9822(00)80115-3 Wainright, 1993, Monophyletic origin of the metazoa, Science, 260, 340, 10.1126/science.8469985 Poirier, 1999, Immune-associated nucleotide-1 (IAN-1) is a thymic selection marker and defines a novel gene family conserved in plants, J. Immunol., 163, 4960, 10.4049/jimmunol.163.9.4960 Reuber, 1996, Isolation of Arabidopsis genes that differentiate between resistance responses mediated by the RPS2 and RPM1 disease resistance genes, Plant Cell, 8, 241, 10.1105/tpc.8.2.241 Gutensohn, 2000, Functional analysis of the two Arabidopsis homologues of Toc34, a component of the chloroplast protein import apparatus, Plant J., 23, 771, 10.1046/j.1365-313x.2000.00849.x Spormann, 1999, Gliding mutants of Myxococcus xanthus with high reversal frequencies and small displacements, J. Bacteriol., 181, 2593, 10.1128/JB.181.8.2593-2601.1999 Koonin, 2000, Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation, Curr. Biol., 10, R774, 10.1016/S0960-9822(00)00774-0 Aravind, 2001, Apoptotic molecular machinery, Science, 291, 1279, 10.1126/science.291.5507.1279 Mocz, 2001, Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases, Structure, 9, 93, 10.1016/S0969-2126(00)00557-8 Endow, 1999, Microtubule motors in spindle and chromosome motility, Eur. J. Biochem., 262, 12, 10.1046/j.1432-1327.1999.00339.x Sack, 1999, Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites, Eur. J. Biochem., 262, 1, 10.1046/j.1432-1327.1999.00341.x Kull, 1996, Crystal structure of the kinesin motor domain reveals a structural similarity to myosin, Nature, 380, 550, 10.1038/380550a0 Racevskis, 1996, Cloning of a novel nucleolar guanosine 5′- triphosphate binding protein autoantigen from a breast tumor, Cell Growth Differ., 7, 271 Draper, 1999, RNA binding strategies of ribosomal proteins, Nucl. Acids Res., 27, 381, 10.1093/nar/27.2.381 Ponting, 1995, Swaposins, Trends Biochem. Sci., 20, 179, 10.1016/S0968-0004(00)89003-9 Pan, 1993, Circularly permuted DNA, RNA and proteins – a review, Gene, 125, 111, 10.1016/0378-1119(93)90317-V Urrutia, 1997, The dynamins, Proc. Natl Acad. Sci. USA, 94, 377, 10.1073/pnas.94.2.377 van Der Bliek, 2000, A mitochondrial division apparatus takes shape, J. Cell Biol., 151, F1, 10.1083/jcb.151.2.F1 Schmid, 1998, Dynamin and its partners, Curr. Opin. Cell Biol., 10, 504, 10.1016/S0955-0674(98)80066-5 Pitossi, 1993, A functional GTP-binding motif is necessary for antiviral activity of Mx proteins, J. Virol., 67, 6726, 10.1128/JVI.67.11.6726-6732.1993 van der Bliek, 1999, Functional diversity in the dynamin family, Trends Cell Biol., 9, 96, 10.1016/S0962-8924(98)01490-1 Sever, 1999, Impairment of dynamin’s GAP domain stimulates receptor-mediated endocytosis, Nature, 398, 481, 10.1038/19024 Stowell, 1999, Nucleotide-dependent conformational changes in dynamin, Nature Cell Biol., 1, 27, 10.1038/8997 Sever, 2000, Dynamin, J. Cell Biol., 150, 1137, 10.1083/jcb.150.5.1137 Hermann, 1998, Mitochondrial fusion in yeast requires the transmembrane GTPase Fzo1p, J. Cell Biol., 143, 359, 10.1083/jcb.143.2.359 Sesaki, 1999, Division versus fusion, J. Cell Biol., 147, 699, 10.1083/jcb.147.4.699 Prakash, 2000, Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism, EMBO J., 19, 4555, 10.1093/emboj/19.17.4555 Parker, 2000, Genetic interactions during root hair morphogenesis in Arabidopsis, Plant Cell, 12, 1961, 10.1105/tpc.12.10.1961 Inoue, 1997, A novel RING finger protein, BFP, predominantly expressed in the brain, Biochem. Biophys. Res. Commun., 240, 8, 10.1006/bbrc.1997.7589 Zhou, 2000, Structure of the ArsA ATPase, EMBO J., 19, 4838, 10.1093/emboj/19.17.4838 Schindelin, 1997, Structure of ADP×AIF4(−)-stabilized nitrogenase complex and its implications for signal transduction, Nature, 387, 370, 10.1038/387370a0 Hayashi, 2001, Structural and functional studies of MinD ATPase, EMBO J., 20, 1819, 10.1093/emboj/20.8.1819 Koonin, 1993, A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif, J. Mol. Biol., 229, 1165, 10.1006/jmbi.1993.1115 Vitale, 1996, NBP35 encodes an essential and evolutionary conserved protein in Saccharomyces cerevisiae with homology to a superfamily of bacterial ATPases, Gene, 178, 97, 10.1016/0378-1119(96)00341-1 Gerard, 1998, Isolation of a minD-like gene in the hyperthermophilic archaeon Pyrococcus AL585, and phylogenetic characterization of related proteins in the three domains of life, Gene, 222, 99, 10.1016/S0378-1119(98)00471-5 Nakashima, 1999, Two novel mouse genes – Nubp2, mapped to the t-complex on chromosome 17, and Nubp1, mapped to chromosome 16 – establish a new gene family of nucleotide-binding proteins in eukaryotes, Genomics, 60, 152, 10.1006/geno.1999.5898 de Boer, 1991, The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site, EMBO J., 10, 4371, 10.1002/j.1460-2075.1991.tb05015.x Wakasugi, 1997, Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris, Proc. Natl Acad. Sci. USA, 94, 5967, 10.1073/pnas.94.11.5967 Turmel, 1999, The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea, Proc. Natl Acad. Sci. USA, 96, 10248, 10.1073/pnas.96.18.10248 Campos-Garcia, 2000, The pseudomonas aeruginosa motR gene involved in regulation of bacterial motility, FEMS Microbiol. Letters, 184, 57, 10.1016/S0378-1097(00)00019-7 Motallebi-Veshareh, 1990, A family of ATPases involved in active partitioning of diverse bacterial plasmids, Mol. Microbiol., 4, 1455, 10.1111/j.1365-2958.1990.tb02056.x Mohl, 1997, Cell cycle-dependent polar localization of chromosome partitioning proteins in Caulobacter crescentus, Cell, 88, 675, 10.1016/S0092-8674(00)81910-8 Kim, 2000, Partitioning of the linear chromosome during sporulation of Streptomyces coelicolor A3(2) involves an oriC-linked parAB locus, J. Bacteriol., 182, 1313, 10.1128/JB.182.5.1313-1320.2000 Quisel, 2000, Control of sporulation gene expression in Bacillus subtilis by the chromosome partitioning proteins Soj (ParA) and Spo0 J (ParB), J. Bacteriol., 182, 3446, 10.1128/JB.182.12.3446-3451.2000 Ireton, 1994, spo0 J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis, J. Bacteriol., 176, 5320, 10.1128/jb.176.17.5320-5329.1994 Suzuki, 1992, Light-independent chlorophyll biosynthesis, Plant Cell, 4, 929, 10.1105/tpc.4.8.929 Rosen, 1990, The plasmid-encoded arsenical resistance pump, Res. Microbiol., 141, 336, 10.1016/0923-2508(90)90008-E Chen, 1986, Nucleotide sequence of the structural genes for an anion pump. The plasmid-encoded arsenical resistance operon, J. Biol. Chem., 261, 15030, 10.1016/S0021-9258(18)66824-3 Suzuki, 1998, Expression and regulation of the arsenic resistance operon of Acidiphilium multivorum AIU 301 plasmid pKW301 in Escherichia coli, Appl. Environ. Microbiol., 64, 411, 10.1128/AEM.64.2.411-418.1998 Ng, 1998, Snapshot of a large dynamic replicon in a halophilic archaeon, Genome Res., 8, 1131, 10.1101/gr.8.11.1131 Rosen, 1999, Families of arsenic transporters, Trends Microbiol., 7, 207, 10.1016/S0966-842X(99)01494-8 Wugeditsch, 2001, Phosphorylation of Wzc, a tyrosine autokinase, is essential for assembly of group 1 capsular polysaccharides in Escherichia coli, J. Biol. Chem., 276, 2361, 10.1074/jbc.M009092200 Ilan, 1999, Protein tyrosine kinases in bacterial pathogens are associated with virulence and production of exopolysaccharide, EMBO J., 18, 3241, 10.1093/emboj/18.12.3241 Vincent, 1999, Cells of Escherichia coli contain a protein-tyrosine kinase, Wzc, and a phosphotyrosine-protein phosphatase, Wzb, J. Bacteriol., 181, 3472, 10.1128/JB.181.11.3472-3477.1999 Vincent, 2000, Relationship between exopolysaccharide production and protein-tyrosine phosphorylation in Gram-negative bacteria, J. Mol. Biol., 304, 311, 10.1006/jmbi.2000.4217 Yang, 1997, Active site mutants of Escherichia coli dethiobiotin synthetase, Biochemistry, 36, 4751, 10.1021/bi9631677 Eisenberg, 1979, Dethiobiotin synthetase, Methods Enzymol., 62, 348, 10.1016/0076-6879(79)62241-3 Huang, 1995, Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate, Biochemistry, 34, 10985, 10.1021/bi00035a004 Galperin, 2000, The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase, Proteins: Struct. Funct. Genet., 41, 238, 10.1002/1097-0134(20001101)41:2<238::AID-PROT80>3.0.CO;2-L Weng, 1986, Nucleotide sequence of Escherichia coli pyrG encoding CTP synthetase, J. Biol. Chem., 261, 5568, 10.1016/S0021-9258(19)57252-0 Pappas, 1999, Characterization of a novel dUTP-dependent activity of CTP synthetase from Saccharomyces cerevisiae, Biochemistry, 38, 16671, 10.1021/bi9920127 Blanche, 1991, Biosynthesis of vitamin B12, J. Bacteriol., 173, 6046, 10.1128/jb.173.19.6046-6051.1991 Honzatko, 1999, Structure-function studies of adenylosuccinate synthetase from Escherichia coli, Arch. Biochem. Biophys., 370, 1, 10.1006/abbi.1999.1383 Natale, 2000, Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs), Genome Biol., 1, 10.1186/gb-2000-1-5-research0009 Radfar, 2000, The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica, Biochemistry, 39, 3920, 10.1021/bi992790z Kounga, 1996, Site-directed mutagenesis of putative catalytic and nucleotide binding sites in N10-formyltetrahydrofolate synthetase, Biochim. Biophys. Acta, 1296, 112, 10.1016/0167-4838(96)00059-3 Zopf, 1990, The methionine-rich domain of the 54 kd protein subunit of the signal recognition particle contains an RNA binding site and can be crosslinked to a signal sequence, EMBO J., 9, 4511, 10.1002/j.1460-2075.1990.tb07902.x Keenan, 1998, Crystal structure of the signal sequence binding subunit of the signal recognition particle, Cell, 94, 181, 10.1016/S0092-8674(00)81418-X de Leeuw, 2000, Anionic phospholipids are involved in membrane association of FtsY and stimulate its GTPase activity, EMBO J., 19, 531, 10.1093/emboj/19.4.531 Gribaldo, 1998, The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery, J. Mol. Evol., 47, 508, 10.1007/PL00006407 Carpenter, 1992, flhF, a Bacillus subtilis flagellar gene that encodes a putative GTP-binding protein, Mol. Microbiol., 6, 2705, 10.1111/j.1365-2958.1992.tb01447.x Koonin, 1996, Escherichia coli - functional and evolutionary implications of genome scale computer-aided protein sequence analysis Lee, 1992, Klebsiella aerogenes urease gene cluster, J. Bacteriol., 174, 4324, 10.1128/jb.174.13.4324-4330.1992 Lutz, 1991, Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli, Mol. Microbiol., 5, 123, 10.1111/j.1365-2958.1991.tb01833.x Colbeau, 1993, Organization of the genes necessary for hydrogenase expression in Rhodobacter capsulatus. Sequence analysis and identification of two hyp regulatory mutants, Mol. Microbiol., 8, 15, 10.1111/j.1365-2958.1993.tb01199.x Maier, 1993, The product of the hypB gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein, J. Bacteriol., 175, 630, 10.1128/jb.175.3.630-635.1993 Fu, 1995, HypB protein of Bradyrhizobium japonicum is a metal-binding GTPase capable of binding 18 divalent nickel ions per dimer, Proc. Natl Acad. Sci. USA, 92, 2333, 10.1073/pnas.92.6.2333 Crouzet, 1991, J. Bacteriol., 173, 6074, 10.1128/jb.173.19.6074-6087.1991 Celis, 1998, Phosphorylation of the periplasmic binding protein in two transport systems for arginine incorporation in Escherichia coli K-12 is unrelated to the function of the transport system, J. Bacteriol., 180, 4828, 10.1128/JB.180.18.4828-4833.1998 El-Moghazy, 2000, Functional analysis of six novel ORFs on the left arm of chromosome XII in Saccharomyces cerevisiae reveals two essential genes, one of which is under cell-cycle control, Yeast, 16, 277, 10.1002/(SICI)1097-0061(200002)16:3<277::AID-YEA524>3.0.CO;2-G Minvielle-Sebastia, 1997, The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3′-end formation, Proc. Natl Acad. Sci. USA, 94, 7897, 10.1073/pnas.94.15.7897 Nitta, 2000, A novel cytoplasmic GTPase XAB1 interacts with DNA repair protein XPA, Nucl. Acids Res., 28, 4212, 10.1093/nar/28.21.4212 Leipe, 1999, Did DNA replication evolve twice independently?, Nucl. Acids Res., 27, 3389, 10.1093/nar/27.17.3389 Altschul, 1997, Gapped BLAST and PSI-BLAST, Nucl. Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Altschul, 1998, Iterated profile searches with PSI-BLAST – a tool for discovery in protein databases, Trends Biochem. Sci., 23, 444, 10.1016/S0968-0004(98)01298-5 Jeanmougin, 1998, Multiple sequence alignment with Clustal X, Trends Biochem. Sci., 23, 403, 10.1016/S0968-0004(98)01285-7 Tatusov, 2001, The COG database, Nucl. Acids Res., 29, 22, 10.1093/nar/29.1.22 Adachi, 1996 Jones, 1992, The rapid generation of mutation data matrices from protein sequences, Comput. Appl. Biosci., 8, 275 Strimmer, 1996, Quartet puzzling, Mol. Biol. Evol., 13, 964, 10.1093/oxfordjournals.molbev.a025664 Henikoff, 1992, Amino acid substitution matrices from protein blocks, Proc. Natl Acad. Sci. USA, 89, 10915, 10.1073/pnas.89.22.10915 Saitou, 1987, The neighbor-joining method, Mol. Biol. Evol., 4, 406 Gibrat, 1996, Surprising similarities in structure comparison, Curr. Opin. Struct. Biol., 6, 377, 10.1016/S0959-440X(96)80058-3 Madej, 1995, Threading a database of protein cores, Proteins: Struct. Funct. Genet., 23, 356, 10.1002/prot.340230309 Holm, 1996, Mapping the protein universe, Science, 273, 595, 10.1126/science.273.5275.595