-
1
-
-
18744382506
-
Prottest: Selection of best-fit models of protein evolution
-
Abascal, F., R. Zardoya, and D. Posada. 2005. Prottest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
0038681416
-
Diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from groundwater and aquifer microorganisms
-
Alfreider, A., C. Vogt, D. Hoffmann, and W. Babel. 2003. Diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from groundwater and aquifer microorganisms. Microb. Ecol. 45:317-328.
-
(2003)
Microb. Ecol
, vol.45
, pp. 317-328
-
-
Alfreider, A.1
Vogt, C.2
Hoffmann, D.3
Babel, W.4
-
3
-
-
0037304408
-
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins
-
Anantharaman, V., L. Aravind, and E. V. Koonin. 2003. Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. Curr. Opin. Chem. Biol. 7:12-20.
-
(2003)
Curr. Opin. Chem. Biol
, vol.7
, pp. 12-20
-
-
Anantharaman, V.1
Aravind, L.2
Koonin, E.V.3
-
4
-
-
0030003964
-
Large structures at high resolution: The 1.6 Å crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate
-
Andersson, I. 1996. Large structures at high resolution: the 1.6 Å crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate. J. Mol. Biol. 259:160-174.
-
(1996)
J. Mol. Biol
, vol.259
, pp. 160-174
-
-
Andersson, I.1
-
5
-
-
0037561915
-
Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase
-
Andersson, I., and T. C. Taylor. 2003. Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch. Biochem. Biophys. 414:130-140.
-
(2003)
Arch. Biochem. Biophys
, vol.414
, pp. 130-140
-
-
Andersson, I.1
Taylor, T.C.2
-
6
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
Andreeva, A., D. Howorth, S. E. Brenner, T. J. Hubbard, C. Chothia, and A. G. Murzin. 2004. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32:D226-229.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
7
-
-
20444419762
-
Was photosynthetic Rubisco recruited by acquisitive evolution from Rubisco-like proteins involved in sulfur metabolism?
-
Ashida, H., A. Danchin, and A. Yokota. 2005. Was photosynthetic Rubisco recruited by acquisitive evolution from Rubisco-like proteins involved in sulfur metabolism? Res. Microbiol. 156:611-618.
-
(2005)
Res. Microbiol
, vol.156
, pp. 611-618
-
-
Ashida, H.1
Danchin, A.2
Yokota, A.3
-
8
-
-
0141993683
-
A functional link between Rubisco-like protein of Bacillus and photosynthetic Rubisco
-
Ashida, H., Y. Saito, C. Kojima, K. Kobayashi, N. Ogasawara, and A. Yokota. 2003. A functional link between Rubisco-like protein of Bacillus and photosynthetic Rubisco. Science 302:286-290.
-
(2003)
Science
, vol.302
, pp. 286-290
-
-
Ashida, H.1
Saito, Y.2
Kojima, C.3
Kobayashi, K.4
Ogasawara, N.5
Yokota, A.6
-
9
-
-
21544471514
-
An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent
-
Beatty, J. T., J. Overmann, M. T. Lince, A. K. Manske, A. S. Lang, R. E. Blankenship, C. L. Van Dover, T. A. Martinson, and F. G. Plumley. 2005. An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proc. Natl. Acad. Sci. USA 102:9306-9310.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 9306-9310
-
-
Beatty, J.T.1
Overmann, J.2
Lince, M.T.3
Manske, A.K.4
Lang, A.S.5
Blankenship, R.E.6
Van Dover, C.L.7
Martinson, T.A.8
Plumley, F.G.9
-
10
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
Bowers, P. M., M. Pellegrini, M. J. Thompson, J. Fierro, T. O. Yeates, and D. Eisenberg. 2004. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 5:R35.
-
(2004)
Genome Biol
, vol.5
-
-
Bowers, P.M.1
Pellegrini, M.2
Thompson, M.J.3
Fierro, J.4
Yeates, T.O.5
Eisenberg, D.6
-
11
-
-
33747687786
-
A new Rubisco-like protein coexists with a photosynthetic Rubisco in the planktonic cyanobacteria Microcystis
-
Carre-Mlouka, A., A. Mejean, P. Quillardet, H. Ashida, Y. Saito, A. Yokota, I. Callebaut, A. Sekowska, E. Dittmann, C. Bouchier, and N. T. de Marsac. 2006. A new Rubisco-like protein coexists with a photosynthetic Rubisco in the planktonic cyanobacteria Microcystis. J. Biol. Chem. 281:24462-24471.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 24462-24471
-
-
Carre-Mlouka, A.1
Mejean, A.2
Quillardet, P.3
Ashida, H.4
Saito, Y.5
Yokota, A.6
Callebaut, I.7
Sekowska, A.8
Dittmann, E.9
Bouchier, C.10
de Marsac, N.T.11
-
12
-
-
37349044305
-
Sulfur oxidation in Chlorobium tepidum (syn. Chlorobaculum tepidum): Genetic and proteomic analyses
-
C. Dahl and C. G. Friedrich ed, in press. Springer, New York, NY
-
Chan, L. K., R. Morgan-Kiss, and T. E. Hanson. Sulfur oxidation in Chlorobium tepidum (syn. Chlorobaculum tepidum): genetic and proteomic analyses. In C. Dahl and C. G. Friedrich (ed.), Proceedings of the International Symposium on Microbial Sulfur Metabolism, in press. Springer, New York, NY.
-
Proceedings of the International Symposium on Microbial Sulfur Metabolism
-
-
Chan, L.K.1
Morgan-Kiss, R.2
Hanson, T.E.3
-
13
-
-
0000672797
-
Mechanism of RubisCO: The carbamate as general base
-
Cleland, W. W., J. T. Andrews, S. Gutteridge, F. C. Hartman, and G. H. Lorimer. 1998. Mechanism of RubisCO: the carbamate as general base. Chem. Rev. 98:549-561.
-
(1998)
Chem. Rev
, vol.98
, pp. 549-561
-
-
Cleland, W.W.1
Andrews, J.T.2
Gutteridge, S.3
Hartman, F.C.4
Lorimer, G.H.5
-
14
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar, T., B. Snel, M. Huynen, and P. Bork. 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23:324-328.
-
(1998)
Trends Biochem. Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
15
-
-
0026559592
-
The consistency of several phytogeny-inference methods under varying evolutionary rates
-
DeBry, R. W. 1992. The consistency of several phytogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol. 9:537-551.
-
(1992)
Mol. Biol. Evol
, vol.9
, pp. 537-551
-
-
DeBry, R.W.1
-
16
-
-
0029897169
-
Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids
-
Delwiche, C. F., and J. D. Palmer. 1996. Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13:873-882.
-
(1996)
Mol. Biol. Evol
, vol.13
, pp. 873-882
-
-
Delwiche, C.F.1
Palmer, J.D.2
-
17
-
-
33746830079
-
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features
-
Derelle, E., C. Ferraz, S. Rombauts, P. Rouze, A. Z. Worden, S. Robbens, F. Partensky, S. Degroeve, S. Echeynie, R. Cooke, Y. Saeys, J. Wuyts, K. Jabbari, C. Bowler, O. Panaud, B. Piegu, S. G. Ball, J. P. Ral, F. Y. Beuget, G. Piganeau, B. De Baets, A. Picard, M. Delseny, J. Demaille, Y. Van de Peer, and H. Moreau. 2006. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. USA 103:11647-11652.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 11647-11652
-
-
Derelle, E.1
Ferraz, C.2
Rombauts, S.3
Rouze, P.4
Worden, A.Z.5
Robbens, S.6
Partensky, F.7
Degroeve, S.8
Echeynie, S.9
Cooke, R.10
Saeys, Y.11
Wuyts, J.12
Jabbari, K.13
Bowler, C.14
Panaud, O.15
Piegu, B.16
Ball, S.G.17
Ral, J.P.18
Beuget, F.Y.19
Piganeau, G.20
De Baets, B.21
Picard, A.22
Delseny, M.23
Demaille, J.24
Van de Peer, Y.25
Moreau, H.26
more..
-
18
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
19
-
-
2642524290
-
2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation
-
2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation. FEMS Microbiol. Rev. 28:353-376.
-
(2004)
FEMS Microbiol. Rev
, vol.28
, pp. 353-376
-
-
Dubbs, J.M.1
Tabita, F.R.2
-
20
-
-
0034685616
-
The transition between the open and closed states of Rubisco is triggered by the inter-phosphate distance of the bound bisphosphate
-
Duff, A. P., T. J. Andrews, and P. M. Curmi. 2000. The transition between the open and closed states of Rubisco is triggered by the inter-phosphate distance of the bound bisphosphate. J. Mol. Biol. 298:903-916.
-
(2000)
J. Mol. Biol
, vol.298
, pp. 903-916
-
-
Duff, A.P.1
Andrews, T.J.2
Curmi, P.M.3
-
21
-
-
49249144575
-
Most abundant protein in the world
-
Ellis, R. J. 1979. Most abundant protein in the world. Trends Biochem. Sci. 4:241-244.
-
(1979)
Trends Biochem. Sci
, vol.4
, pp. 241-244
-
-
Ellis, R.J.1
-
22
-
-
0035318376
-
Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms
-
Elsaied, H., and T. Naganuma. 2001. Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Appl. Environ. Microbiol. 67:1751-1765.
-
(2001)
Appl. Environ. Microbiol
, vol.67
, pp. 1751-1765
-
-
Elsaied, H.1
Naganuma, T.2
-
23
-
-
33846137706
-
Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems
-
Elsaied, H. E., H. Kimura, and T. Naganuma. 2007. Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems. Extremophiles 11:191-202.
-
(2007)
Extremophiles
, vol.11
, pp. 191-202
-
-
Elsaied, H.E.1
Kimura, H.2
Naganuma, T.3
-
24
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright, A. J., I. Iliopoulos, N. C. Kyrpides, and C. A. Ouzounis. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
25
-
-
0033582465
-
Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1
-
Ezaki, S., N. Maeda, T. Kishimoto, H. Atomi, and T. Imanaka. 1999. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J. Biol. Chem. 274:5078-5082.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 5078-5082
-
-
Ezaki, S.1
Maeda, N.2
Kishimoto, T.3
Atomi, H.4
Imanaka, T.5
-
26
-
-
4544272017
-
Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea
-
Finn, M. W., and F. R. Tabita. 2004. Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea. J. Bacteriol. 186:6360-6366.
-
(2004)
J. Bacteriol
, vol.186
, pp. 6360-6366
-
-
Finn, M.W.1
Tabita, F.R.2
-
27
-
-
0038643328
-
Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea
-
Finn, M. W., and F. R. Tabita. 2003. Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea. J. Bacteriol. 185:3049-3059.
-
(2003)
J. Bacteriol
, vol.185
, pp. 3049-3059
-
-
Finn, M.W.1
Tabita, F.R.2
-
28
-
-
0344885455
-
2 fixation in chemotrophic anaerobic bacteria
-
H. W. Van Verseveld and J. A. Duine ed, compounds. Martinus Nijhoff, Dordrecht, The Netherlands
-
1 compounds. Martinus Nijhoff, Dordrecht, The Netherlands.
-
(1987)
1
, pp. 39-43
-
-
Fuchs, G.1
Lange, S.2
Rude, E.3
Schaefer, S.4
Schauder, R.5
Scholtz, R.6
Stupperich, E.7
-
29
-
-
0017620115
-
Different molecular forms of D-ribulose-1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides
-
Gibson, J. L., and F. R. Tabita. 1977. Different molecular forms of D-ribulose-1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides. J. Biol. Chem. 252:943-949.
-
(1977)
J. Biol. Chem
, vol.252
, pp. 943-949
-
-
Gibson, J.L.1
Tabita, F.R.2
-
30
-
-
0347506350
-
Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the Rubisco-like protein
-
Hanson, T. E., and F. R. Tabita. 2003. Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the Rubisco-like protein. Photosynth. Res. 78:231-248.
-
(2003)
Photosynth. Res
, vol.78
, pp. 231-248
-
-
Hanson, T.E.1
Tabita, F.R.2
-
31
-
-
0035836695
-
A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress
-
Hanson, T. E., and F. R. Tabita. 2001. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc. Natl. Acad. Sci. USA 98:4397-4402.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 4397-4402
-
-
Hanson, T.E.1
Tabita, F.R.2
-
32
-
-
0028245595
-
Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase
-
Hartman, F. C., and M. R. Harpel. 1994. Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Annu. Rev. Biochem. 63:197-234.
-
(1994)
Annu. Rev. Biochem
, vol.63
, pp. 197-234
-
-
Hartman, F.C.1
Harpel, M.R.2
-
33
-
-
34047237283
-
Mechanistic diversity in the RuBisCO superfamily: The "enolase" in the methionine salvage pathway in Geobacillus kaustophilus
-
Imker, H. J., A. A. Fedorov, E. V. Fedorov, S. C. Almo, and J. A. Gerlt. 2007. Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus. Biochemistry 46:4077-4089.
-
(2007)
Biochemistry
, vol.46
, pp. 4077-4089
-
-
Imker, H.J.1
Fedorov, A.A.2
Fedorov, E.V.3
Almo, S.C.4
Gerlt, J.A.5
-
34
-
-
33746645973
-
Gene diversity and organization in rbcL-containing genome fragments from uncultivated Synechococcus in the Gulf of Mexico
-
John, D. E., B. Wawrik, F. Tabita, and J. H. Paul. 2006. Gene diversity and organization in rbcL-containing genome fragments from uncultivated Synechococcus in the Gulf of Mexico. Mar. Ecol. Prog. Ser. 316:23-33.
-
(2006)
Mar. Ecol. Prog. Ser
, vol.316
, pp. 23-33
-
-
John, D.E.1
Wawrik, B.2
Tabita, F.3
Paul, J.H.4
-
35
-
-
0025160560
-
Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site
-
Knight, S., I. Andersson, and C. I. Branden. 1990. Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site. J. Mol. Biol. 215:113-160.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 113-160
-
-
Knight, S.1
Andersson, I.2
Branden, C.I.3
-
36
-
-
0033537899
-
Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts
-
Kopp, J., S. Kopriva, K. H. Suss, and G. E. Schulz. 1999. Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. J. Mol. Biol. 287:761-771.
-
(1999)
J. Mol. Biol
, vol.287
, pp. 761-771
-
-
Kopp, J.1
Kopriva, S.2
Suss, K.H.3
Schulz, G.E.4
-
38
-
-
3242810318
-
MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
-
Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
-
(2004)
Brief. Bioinform
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
39
-
-
18944389308
-
Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum
-
Li, H., M. R. Sawaya, F. R. Tabita, and D. Eisenberg. 2005. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 13:779-789.
-
(2005)
Structure
, vol.13
, pp. 779-789
-
-
Li, H.1
Sawaya, M.R.2
Tabita, F.R.3
Eisenberg, D.4
-
40
-
-
0027943051
-
Transcription control of ribulose bisphosphate carboxylase/oxygenase activase and adjacent genes in Anabaena species
-
Li, L. A., and F. R. Tabita. 1994. Transcription control of ribulose bisphosphate carboxylase/oxygenase activase and adjacent genes in Anabaena species. J. Bacteriol. 176:6697-6706.
-
(1994)
J. Bacteriol
, vol.176
, pp. 6697-6706
-
-
Li, L.A.1
Tabita, F.R.2
-
41
-
-
34047169728
-
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
-
Lo, I., V. J. Denef, N. C. Verberkmoes, M. B. Shah, D. Goltsman, G. DiBartolo, G. W. Tyson, E. E. Allen, R. J. Ram, J. C. Detter, P. Richardson, M. P. Thelen, R. L. Hettich, and J. F. Banfleld. 2007. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537-541.
-
(2007)
Nature
, vol.446
, pp. 537-541
-
-
Lo, I.1
Denef, V.J.2
Verberkmoes, N.C.3
Shah, M.B.4
Goltsman, D.5
DiBartolo, G.6
Tyson, G.W.7
Allen, E.E.8
Ram, R.J.9
Detter, J.C.10
Richardson, P.11
Thelen, M.P.12
Hettich, R.L.13
Banfleld, J.F.14
-
43
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E. M., M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
44
-
-
0028977898
-
A nuclear-encoded form II RuBisCO in dinoflagellates
-
Morse, D., P. Salois, P. Markovic, and J. W. Hastings. 1995. A nuclear-encoded form II RuBisCO in dinoflagellates. Science 268:1622- 1624.
-
(1995)
Science
, vol.268
, pp. 1622-1624
-
-
Morse, D.1
Salois, P.2
Markovic, P.3
Hastings, J.W.4
-
45
-
-
0036202171
-
Prediction of gene function in methylthioadenosine recycling from regulatory signals
-
Murphy, B. A., F. J. Grundy, and T. M. Henkin. 2002. Prediction of gene function in methylthioadenosine recycling from regulatory signals. J. Bacteriol. 184:2314-2318.
-
(2002)
J. Bacteriol
, vol.184
, pp. 2314-2318
-
-
Murphy, B.A.1
Grundy, F.J.2
Henkin, T.M.3
-
46
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano, N., C. A. Orengo, and J. M. Thornton. 2002. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321:741-765.
-
(2002)
J. Mol. Biol
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
47
-
-
2942608404
-
Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase
-
Nanba, K., G. M. King, and K. Dunfield. 2004. Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl. Environ. Microbiol. 70:2245-2253.
-
(2004)
Appl. Environ. Microbiol
, vol.70
, pp. 2245-2253
-
-
Nanba, K.1
King, G.M.2
Dunfield, K.3
-
48
-
-
0347719528
-
Evaluation of protein fold comparison servers
-
Novotny, M., D. Madsen, and G. J. Kleywegt. 2004. Evaluation of protein fold comparison servers. Proteins 54:260-270.
-
(2004)
Proteins
, vol.54
, pp. 260-270
-
-
Novotny, M.1
Madsen, D.2
Kleywegt, G.J.3
-
49
-
-
0034714290
-
Activase region on chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Nonconservative substitution in the large subunit alters species specificity of protein interaction
-
Ott, C. M., B. D. Smith, A. R. Portis, Jr., and R. J. Spreitzer. 2000. Activase region on chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Nonconservative substitution in the large subunit alters species specificity of protein interaction. J. Biol. Chem. 275:26241- 26244.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 26241-26244
-
-
Ott, C.M.1
Smith, B.D.2
Portis Jr., A.R.3
Spreitzer, R.J.4
-
50
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek, R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96:2896-2901.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
51
-
-
0029608860
-
Rubisco rules fall; gene transfer triumphs
-
Palmer, J. D. 1995. Rubisco rules fall; gene transfer triumphs. Bioessays 17:1005-1008.
-
(1995)
Bioessays
, vol.17
, pp. 1005-1008
-
-
Palmer, J.D.1
-
52
-
-
0030098202
-
Rubisco surprises in dinoflagellates
-
Palmer, J. D. 1996. Rubisco surprises in dinoflagellates. Plant Cell 8:343-345.
-
(1996)
Plant Cell
, vol.8
, pp. 343-345
-
-
Palmer, J.D.1
-
53
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96:4285-4288.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
54
-
-
0036160526
-
Computational method to assign microbial genes to pathways
-
Pellegrini, M., M. Thompson, J. Fierro, and P. Bowers. 2001. Computational method to assign microbial genes to pathways. J. Cell. Biochem. Suppl. 37:106-109.
-
(2001)
J. Cell. Biochem. Suppl
, vol.37
, pp. 106-109
-
-
Pellegrini, M.1
Thompson, M.2
Fierro, J.3
Bowers, P.4
-
55
-
-
0030868741
-
Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities
-
Pichard, S. L., L. Campbell, and J. H. Paul. 1997. Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities. Appl. Environ. Microbiol. 63:3600-3606.
-
(1997)
Appl. Environ. Microbiol
, vol.63
, pp. 3600-3606
-
-
Pichard, S.L.1
Campbell, L.2
Paul, J.H.3
-
56
-
-
0030800147
-
Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes
-
Rhee, S., K. D. Parris, C. C. Hyde, S. A. Ahmed, E. W. Miles, and D. R. Davies. 1997. Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes. Biochemistry 36:7664-7680.
-
(1997)
Biochemistry
, vol.36
, pp. 7664-7680
-
-
Rhee, S.1
Parris, K.D.2
Hyde, C.C.3
Ahmed, S.A.4
Miles, E.W.5
Davies, D.R.6
-
57
-
-
34047227131
-
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: Organelle genomes of the smallest eukaryote are examples of compaction
-
Robbens, S., E. Derelle, C. Ferraz, J. Wuyts, H. Moreau, and Y. Van de Peer. 2007. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol. Biol. Evol. 24:956-968.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 956-968
-
-
Robbens, S.1
Derelle, E.2
Ferraz, C.3
Wuyts, J.4
Moreau, H.5
Van de Peer, Y.6
-
58
-
-
0030096623
-
Rubisco in marine symbiotic dinoflagellates: Form II enzymes in eukaryotic oxygenic phototrophs encoded by a nuclear multigene family
-
Rowan, R., S. M. Whitney, A. Fowler, and D. Yellowlees. 1996. Rubisco in marine symbiotic dinoflagellates: form II enzymes in eukaryotic oxygenic phototrophs encoded by a nuclear multigene family. Plant Cell 8:539-553.
-
(1996)
Plant Cell
, vol.8
, pp. 539-553
-
-
Rowan, R.1
Whitney, S.M.2
Fowler, A.3
Yellowlees, D.4
-
59
-
-
33847157932
-
Archaeal type III RuBisCOs function in a pathway for AMP metabolism
-
Sato, T., H. Atomi, and T. Imanaka. 2007. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315:1003-1006.
-
(2007)
Science
, vol.315
, pp. 1003-1006
-
-
Sato, T.1
Atomi, H.2
Imanaka, T.3
-
60
-
-
0038824870
-
-
Saunders, N. F., T. Thomas, P. M. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, R. Feldman, C. Gates, S. Bench, K. Sowers, K. Kadner, A. Aerts, P. Dehal, C. Detter, T. Glavina, S. Lucas, P. Richardson, F. Larimer, L. Hauser, M. Land, and R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:1580-1588.
-
Saunders, N. F., T. Thomas, P. M. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, R. Feldman, C. Gates, S. Bench, K. Sowers, K. Kadner, A. Aerts, P. Dehal, C. Detter, T. Glavina, S. Lucas, P. Richardson, F. Larimer, L. Hauser, M. Land, and R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:1580-1588.
-
-
-
-
62
-
-
0027371878
-
Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form
-
Schreuder, H. A., S. Knight, P. M. Curmi, I. Andersson, D. Cascio, C. I. Branden, and D. Eisenberg. 1993. Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form. Proc. Natl. Acad. Sci. USA 90:9968-9972.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 9968-9972
-
-
Schreuder, H.A.1
Knight, S.2
Curmi, P.M.3
Andersson, I.4
Cascio, D.5
Branden, C.I.6
Eisenberg, D.7
-
63
-
-
19044362589
-
The methionine salvage pathway in Bacillus subtilis
-
Sekowska, A., and A. Danchin. 2002. The methionine salvage pathway in Bacillus subtilis. BMC Microbiol. 2:8.
-
(2002)
BMC Microbiol
, vol.2
, pp. 8
-
-
Sekowska, A.1
Danchin, A.2
-
64
-
-
0023998613
-
Essentiality of Lys-329 of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum as demonstrated by site-directed mutagenesis
-
Soper, T. S., R. J. Mural, F. W. Larimer, E. H. Lee, R. Machanoff, and F. C. Hartman. 1988. Essentiality of Lys-329 of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum as demonstrated by site-directed mutagenesis. Protein Eng. 2:39-44.
-
(1988)
Protein Eng
, vol.2
, pp. 39-44
-
-
Soper, T.S.1
Mural, R.J.2
Larimer, F.W.3
Lee, E.H.4
Machanoff, R.5
Hartman, F.C.6
-
65
-
-
16644364478
-
An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups
-
In Russian
-
Spiridonova, E. M., I. A. Berg, T. V. Kolganova, R. N. Ivanovskii, B. B. Kuznetsov, and T. P. Turova. 2004. An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups. Mikrobiologiia 73:377-387. (In Russian.)
-
(2004)
Mikrobiologiia
, vol.73
, pp. 377-387
-
-
Spiridonova, E.M.1
Berg, I.A.2
Kolganova, T.V.3
Ivanovskii, R.N.4
Kuznetsov, B.B.5
Turova, T.P.6
-
66
-
-
0037001967
-
Rubisco: Structure, regulatory interactions, and possibilities for a better enzyme
-
Spreitzer, R. J., and M. E. Salvucci. 2002. Rubisco: structure, regulatory interactions, and possibilities for a better enzyme. Annu. Rev. Plant Biol. 53:449-475.
-
(2002)
Annu. Rev. Plant Biol
, vol.53
, pp. 449-475
-
-
Spreitzer, R.J.1
Salvucci, M.E.2
-
67
-
-
0000947778
-
2 fixation in purple bacteria
-
R. E. Blankenship, M. T. Madigan, and C. E. Bauer ed, Kluwer Academic Publishers, Dordrecht, The Netherlands
-
2 fixation in purple bacteria, p. 885-914. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
(1995)
Anoxygenic photosynthetic bacteria
, pp. 885-914
-
-
Tabita, F.R.1
-
68
-
-
0032840522
-
Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective
-
Tabita, F. R. 1999. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth. Res. 60:1-28.
-
(1999)
Photosynth. Res
, vol.60
, pp. 1-28
-
-
Tabita, F.R.1
-
69
-
-
0016137330
-
D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. I. Levels, purification, and effects of metallic ions
-
Tabita, F. R., and B. A. McFadden. 1974. D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. I. Levels, purification, and effects of metallic ions. J. Biol. Chem. 249:3453-3458.
-
(1974)
J. Biol. Chem
, vol.249
, pp. 3453-3458
-
-
Tabita, F.R.1
McFadden, B.A.2
-
70
-
-
0016165638
-
-
Tabita, F. R., and B. A. McFadden. 1974. D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. II. Quaternary structure, composition, catalytic, and immunological properties. J. Biol. Chem. 249:3459-3464.
-
Tabita, F. R., and B. A. McFadden. 1974. D-Ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. II. Quaternary structure, composition, catalytic, and immunological properties. J. Biol. Chem. 249:3459-3464.
-
-
-
-
71
-
-
37349063071
-
-
Reference deleted
-
Reference deleted.
-
-
-
-
72
-
-
0035930525
-
First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii
-
Taylor, T. C., A. Backlund, K. Bjorhall, R. J. Spreitzer, and I. Andersson. 2001. First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii. J. Biol. Chem. 276:48159-48164.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 48159-48164
-
-
Taylor, T.C.1
Backlund, A.2
Bjorhall, K.3
Spreitzer, R.J.4
Andersson, I.5
-
73
-
-
0033027258
-
Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic archaea
-
Watson, G. M., J. P. Yu, and F. R. Tabita. 1999. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic archaea. J. Bacteriol. 181:1569-1575.
-
(1999)
J. Bacteriol
, vol.181
, pp. 1569-1575
-
-
Watson, G.M.1
Yu, J.P.2
Tabita, F.R.3
-
74
-
-
0031024440
-
Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A molecule for phylogenetic and enzymological investigation
-
Watson, G. M. F., and F. R. Tabita. 1997. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol. Lett. 146:13-22.
-
(1997)
FEMS Microbiol. Lett
, vol.146
, pp. 13-22
-
-
Watson, G.M.F.1
Tabita, F.R.2
-
75
-
-
0036324122
-
Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes
-
Wawrik, B., J. H. Paul, and F. R. Tabita. 2002. Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl. Environ. Microbiol. 68:3771-3779.
-
(2002)
Appl. Environ. Microbiol
, vol.68
, pp. 3771-3779
-
-
Wawrik, B.1
Paul, J.H.2
Tabita, F.R.3
-
76
-
-
0035896377
-
The TIM-barrel fold: A versatile framework for efficient enzymes
-
Wierenga, R. K. 2001. The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Lett. 492:193-198.
-
(2001)
FEBS Lett
, vol.492
, pp. 193-198
-
-
Wierenga, R.K.1
-
77
-
-
0037177237
-
Homologous (beta/alpha)-barrel enzymes that catalyze unrelated reactions: Orotidine 5′-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase
-
Wise, E., W. S. Yew, P. C. Babbitt, J. A. Gerlt, and I. Rayment. 2002. Homologous (beta/alpha)-barrel enzymes that catalyze unrelated reactions: orotidine 5′-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry 41:3861-3869.
-
(2002)
Biochemistry
, vol.41
, pp. 3861-3869
-
-
Wise, E.1
Yew, W.S.2
Babbitt, P.C.3
Gerlt, J.A.4
Rayment, I.5
-
78
-
-
0030008621
-
Ribulose-1,5-bisphosphate carboxylase/oxygenase gene expression and diversity of Lake Erie planktonic microorganisms
-
Xu, H. H., and F. R. Tabita. 1996. Ribulose-1,5-bisphosphate carboxylase/oxygenase gene expression and diversity of Lake Erie planktonic microorganisms. Appl. Environ. Microbiol. 62:1913-1921.
-
(1996)
Appl. Environ. Microbiol
, vol.62
, pp. 1913-1921
-
-
Xu, H.H.1
Tabita, F.R.2
-
79
-
-
37349051380
-
2 metabolism
-
J. Lederburg ed, 2nd ed. Academic Press Inc, San Diego, CA
-
2 metabolism, p. 349-358. In J. Lederburg (ed.), Encyclopedia of microbiology, 2nd ed. Academic Press Inc., San Diego, CA.
-
(2000)
Encyclopedia of microbiology
, pp. 349-358
-
-
Yoon, K.S.1
Hanson, T.E.2
Gibson, J.L.3
Tabita, F.R.4
-
80
-
-
33947235074
-
-
Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16.
-
Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16.
-
-
-
|