-
1
-
-
0036305943
-
Sequence and structure classification of kinases
-
DOI 10.1016/S0022-2836(02)00538-7
-
S Cheek H Zhang NV Grishin 2002 Sequence and structure classification of kinases J Mol Biol 320 855 881 12095261 10.1016/S0022-2836(02)00538-7 1:CAS:528:DC%2BD38XltVShtL0%3D (Pubitemid 34729411)
-
(2002)
Journal of Molecular Biology
, vol.320
, Issue.4
, pp. 855-881
-
-
Cheek, S.1
Zhang, H.2
Grishin, N.V.3
-
2
-
-
17844401480
-
A comprehensive update of the sequence and structure classification of kinases
-
DOI 10.1186/1472-6807-5-6
-
S Cheek K Ginalski H Zhang NV Grishin 2005 A comprehensive update of the sequence and structure classification of kinases BMC Struct Biol 5 6 15771780 10.1186/1472-6807-5-6 (Pubitemid 40594686)
-
(2005)
BMC Structural Biology
, vol.5
, pp. 6
-
-
Cheek, S.1
Ginalski, K.2
Zhang, H.3
Grishin, N.V.4
-
3
-
-
0032479058
-
1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea
-
DOI 10.1126/science.281.5373.99
-
L Chistoserdova JA Vorholt RK Thauer ME Lidstrom 1998 C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea Science 281 99 102 9651254 10.1126/science.281.5373.99 1:CAS:528:DyaK1cXksVOmsrw%3D (Pubitemid 28354052)
-
(1998)
Science
, vol.281
, Issue.5373
, pp. 99-102
-
-
Chistoserdova, L.1
Vorholt, J.A.2
Thauer, R.K.3
Lidstrom, M.E.4
-
4
-
-
38349134014
-
An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs
-
10.1093/protein/gzm072 18093993 10.1093/protein/gzm072 1:CAS:528:DC%2BD1cXis12ktbs%3D
-
R Counago CJ Wilson MI Pena P Wittung-Stafshede Y Shamoo 2008 An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs Protein Eng Des Sel 21 19 27 10.1093/protein/ gzm072 18093993 10.1093/protein/gzm072 1:CAS:528:DC%2BD1cXis12ktbs%3D
-
(2008)
Protein Eng des Sel
, vol.21
, pp. 19-27
-
-
Counago, R.1
Wilson, C.J.2
Pena, M.I.3
Wittung-Stafshede, P.4
Shamoo, Y.5
-
5
-
-
0038690122
-
Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus
-
DOI 10.1016/S0022-2836(03)00655-7
-
AR Criswell E Bae B Stec J Konisky GN Phillips Jr 2003 Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus J Mol Biol 330 1087 1099 S0022283603006557 12860130 10.1016/S0022-2836(03)00655-7 1:CAS:528:DC%2BD3sXlt1aqu7s%3D (Pubitemid 36818905)
-
(2003)
Journal of Molecular Biology
, vol.330
, Issue.5
, pp. 1087-1099
-
-
Criswell, A.R.1
Bae, E.2
Stec, B.3
Konisky, J.4
Phillips Jr., G.N.5
-
6
-
-
68649113084
-
Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus
-
10.1107/S1744309109024348 19652331 10.1107/S1744309109024348
-
M Davlieva Y Shamoo 2009 Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus Acta Crystallogr Sect F Struct Biol Cryst Commun 65 751 756 10.1107/S1744309109024348 19652331 10.1107/S1744309109024348
-
(2009)
Acta Crystallogr Sect F Struct Biol Cryst Commun
, vol.65
, pp. 751-756
-
-
Davlieva, M.1
Shamoo, Y.2
-
7
-
-
77449125574
-
Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability
-
10.1002/prot.22549 19731371 10.1002/prot.22549 1:CAS:528: DC%2BD1MXhsFGjsr%2FF
-
M Davlieva Y Shamoo 2010 Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability Proteins 78 357 364 10.1002/prot.22549 19731371 10.1002/prot.22549 1:CAS:528:DC%2BD1MXhsFGjsr%2FF
-
(2010)
Proteins
, vol.78
, pp. 357-364
-
-
Davlieva, M.1
Shamoo, Y.2
-
8
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
10.2307/2408678
-
J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791 10.2307/2408678
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
9
-
-
0031051923
-
The adenylate kinase genes of M. voltae, M. thermolithotrophicus, M. jannaschii, and M. igneus define a new family of adenylate kinases
-
DOI 10.1016/S0378-1119(96)00651-8, PII S0378111996006518
-
DM Ferber PJ Haney H Berk D Lynn J Konisky 1997 The adenylate kinase genes of M. voltae, M. thermolithotrophicus, M. jannaschii, and M. igneus define a new family of adenylate kinases Gene 185 239 244 S0378-1119(96)00651-8 9055821 10.1016/S0378-1119(96)00651-8 1:CAS:528:DyaK2sXktFShtw%3D%3D (Pubitemid 27085323)
-
(1997)
Gene
, vol.185
, Issue.2
, pp. 239-244
-
-
Ferber, D.M.1
Haney, P.J.2
Berk, H.3
Lynn, D.4
Konisky, J.5
-
10
-
-
0037870025
-
Global analysis of a "simple" proteome: Methanococcus jannaschii
-
DOI 10.1016/S1570-0232(02)00568-8, PII S1570023202005688
-
CS Giometti, et al. 2002 Global analysis of a "simple" proteome: Methanococcus jannaschii J Chromatogr B Analyt Technol Biomed Life Sci 782 227 243 S1570023202005688 12458009 10.1016/S1570-0232(02)00568-8 1:CAS:528:DC%2BD3sXktFOmsg%3D%3D (Pubitemid 35402029)
-
(2002)
Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences
, vol.782
, Issue.1-2
, pp. 227-243
-
-
Giometti, C.S.1
Reich, C.2
Tollaksen, S.3
Babnigg, G.4
Lim, H.5
Zhu, W.6
Yates III, J.7
Olsen, G.8
-
11
-
-
0026022455
-
Structural characteristics of methanogenic cofactors in the non-methanogenic archaebacterium Archaeoglobus fulgidus
-
1905547 1:CAS:528:DyaK3MXks1yjtL0%3D
-
LG Gorris AC Voet C van der Drift 1991 Structural characteristics of methanogenic cofactors in the non-methanogenic archaebacterium Archaeoglobus fulgidus Biofactors 3 29 35 1905547 1:CAS:528:DyaK3MXks1yjtL0%3D
-
(1991)
Biofactors
, vol.3
, pp. 29-35
-
-
Gorris, L.G.1
Voet, A.C.2
Van Der Drift, C.3
-
12
-
-
0034891038
-
Methanococcus jannaschii generates L-proline by cyclization of L-ornithine
-
DOI 10.1128/JB.183.17.5203-5205.2001
-
M Graupner RH White 2001 Methanococcus jannaschii generates l-proline by cyclization of l-ornithine J Bacteriol 183 5203 5205 11489875 10.1128/JB.183.17.5203-5205.2001 1:CAS:528:DC%2BD3MXmtFKrsLs%3D (Pubitemid 32750950)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.17
, pp. 5203-5205
-
-
Graupner, M.1
White, R.H.2
-
13
-
-
84906299125
-
Biosynthesis of the methanogenic coenzymes
-
T. Begley (eds). Elsevier Amsterdam. 10.1016/B978-008045382-8.00147-7
-
Grochowski LL, White RH (2010) Biosynthesis of the methanogenic coenzymes. In: Begley T (ed) Comprehensive natural products chemistry II. Elsevier, Amsterdam, pp 711-748
-
(2010)
Comprehensive Natural Products Chemistry II
, pp. 711-748
-
-
Grochowski, L.L.1
White, R.H.2
-
14
-
-
33646238682
-
Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate
-
10.1128/JB.188.9.3192-3198.2006 16621811 10.1128/JB.188.9.3192-3198.2006 1:CAS:528:DC%2BD28XktFaiu7g%3D
-
LL Grochowski H Xu RH White 2006 Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate J Bacteriol 188 3192 3198 10.1128/JB.188.9.3192-3198.2006 16621811 10.1128/JB.188.9.3192-3198.2006 1:CAS:528:DC%2BD28XktFaiu7g%3D
-
(2006)
J Bacteriol
, vol.188
, pp. 3192-3198
-
-
Grochowski, L.L.1
Xu, H.2
White, R.H.3
-
15
-
-
0033881465
-
Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea
-
DOI 10.1128/JB.182.17.5013-5016.2000
-
DM Howell M Graupner H Xu RH White 2000 Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea J Bacteriol 182 5013 5016 10940051 10.1128/JB.182.17.5013-5016.2000 1:CAS:528:DC%2BD3cXlvFajurg%3D (Pubitemid 30641832)
-
(2000)
Journal of Bacteriology
, vol.182
, Issue.17
, pp. 5013-5016
-
-
Howell, D.M.1
Graupner, M.2
Xu, H.3
White, R.H.4
-
16
-
-
33947221897
-
Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation
-
DOI 10.1021/bi0618159
-
KS Jensen E Johansson KF Jensen 2007 Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation Biochemistry 46 2745 2757 10.1021/bi0618159 17297917 10.1021/bi0618159 1:CAS:528:DC%2BD2sXhsFOluro%3D (Pubitemid 46417914)
-
(2007)
Biochemistry
, vol.46
, Issue.10
, pp. 2745-2757
-
-
Jensen, K.S.1
Johansson, E.2
Jensen, K.F.3
-
17
-
-
0028823531
-
A secY homologous gene in the crenarchaeon Sulfolobus acidocaldarius
-
7495856
-
T Kath G Schafer 1995 A secY homologous gene in the crenarchaeon Sulfolobus acidocaldarius Biochim Biophys Acta 1264 155 158 7495856
-
(1995)
Biochim Biophys Acta
, vol.1264
, pp. 155-158
-
-
Kath, T.1
Schafer, G.2
-
18
-
-
45949109669
-
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
-
DOI 10.1093/bib/bbn017, Special Issue: Critical Technologies for Bioinformatics
-
S Kumar M Nei J Dudley K Tamura 2008 MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences Brief Bioinform 9 299 306 10.1093/bib/bbn017 18417537 10.1093/bib/bbn017 1:CAS:528:DC%2BD1cXpt1artrg%3D (Pubitemid 351890826)
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.4
, pp. 299-306
-
-
Kumar, S.1
Nei, M.2
Dudley, J.3
Tamura, K.4
-
19
-
-
0027327961
-
Archaebacterial adenylate kinase from the thermoacidophile Sulfolobus acidocaldarius: Purification, characterization, and partial sequence
-
DOI 10.1006/abbi.1993.1229
-
K Lacher G Schafer 1993 Archaebacterial adenylate kinase from the thermoacidophile Sulfolobus acidocaldarius: purification, characterization, and partial sequence Arch Biochem Biophys 302 391 397 10.1006/abbi.1993.1229 8489243 10.1006/abbi.1993.1229 1:CAS:528:DyaK3sXit1yrsLY%3D (Pubitemid 23212688)
-
(1993)
Archives of Biochemistry and Biophysics
, vol.302
, Issue.2
, pp. 391-397
-
-
Lacher, K.1
Schafer, G.2
-
20
-
-
77956227855
-
2+-dependent UMP kinase from Helicobacter pylori
-
10.1007/s00203-010-0600-x 20602229 10.1007/s00203-010-0600-x 1:CAS:528:DC%2BC3cXhtVaqtLnJ
-
2+-dependent UMP kinase from Helicobacter pylori Arch Microbiol 192 739 746 10.1007/s00203-010- 0600-x 20602229 10.1007/s00203-010-0600-x 1:CAS:528:DC%2BC3cXhtVaqtLnJ
-
(2010)
Arch Microbiol
, vol.192
, pp. 739-746
-
-
Lee, M.J.1
Chien-Liang, L.2
Tsai, J.Y.3
Sue, W.T.4
Hsia, W.S.5
Huang, H.6
-
21
-
-
67649887151
-
PGenTHREADER and pDomTHREADER: New methods for improved protein fold recognition and superfamily discrimination
-
10.1093/bioinformatics/btp302 19429599 10.1093/bioinformatics/btp302 1:CAS:528:DC%2BD1MXot1Cjtbc%3D
-
A Lobley MI Sadowski DT Jones 2009 pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination Bioinformatics 25 1761 1767 10.1093/bioinformatics/btp302 19429599 10.1093/bioinformatics/btp302 1:CAS:528:DC%2BD1MXot1Cjtbc%3D
-
(2009)
Bioinformatics
, vol.25
, pp. 1761-1767
-
-
Lobley, A.1
Sadowski, M.I.2
Jones, D.T.3
-
22
-
-
13444259730
-
First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis
-
DOI 10.1016/j.bbapap.2004.11.010
-
C Marco-Marin JM Escamilla-Honrubia V Rubio 2005 First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis Biochim Biophys Acta 1747 271 275 10.1016/j.bbapap.2004.11.010 15698963 1:CAS:528:DC%2BD2MXhtFGltLk%3D (Pubitemid 40215169)
-
(2005)
Biochimica et Biophysica Acta - Proteins and Proteomics
, vol.1747
, Issue.2
, pp. 271-275
-
-
Marco-Marin, C.1
Escamilla-Honrubia, J.M.2
Rubio, V.3
-
23
-
-
23944435947
-
The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis
-
DOI 10.1016/j.jmb.2005.07.045, PII S0022283605008466
-
C Marco-Marin F Gil-Ortiz V Rubio 2005 The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis J Mol Biol 352 438 454 10.1016/j.jmb.2005.07.045 16095620 10.1016/j.jmb.2005.07.045 1:CAS:528:DC%2BD2MXpslyltL4%3D (Pubitemid 41207794)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.2
, pp. 438-454
-
-
Marco-Marin, C.1
Gil-Ortiz, F.2
Rubio, V.3
-
24
-
-
77957672648
-
Archaeal RibL: A new FAD synthetase that is air sensitive
-
10.1021/bi100817q 20822113 10.1021/bi100817q 1:CAS:528:DC%2BC3cXhtFOnsLnF
-
Z Mashhadi H Xu LL Grochowski RH White 2010 Archaeal RibL: a new FAD synthetase that is air sensitive Biochemistry 49 8748 8755 10.1021/bi100817q 20822113 10.1021/bi100817q 1:CAS:528:DC%2BC3cXhtFOnsLnF
-
(2010)
Biochemistry
, vol.49
, pp. 8748-8755
-
-
Mashhadi, Z.1
Xu, H.2
Grochowski, L.L.3
White, R.H.4
-
25
-
-
48749129111
-
The crystal structure of UMP kinase from Bacillus anthracis (BA1797) reveals an allosteric nucleotide-binding site
-
10.1016/j.jmb.2008.06.078 18625239 10.1016/j.jmb.2008.06.078 1:CAS:528:DC%2BD1cXps1Gqurk%3D
-
C Meier, et al. 2008 The crystal structure of UMP kinase from Bacillus anthracis (BA1797) reveals an allosteric nucleotide-binding site J Mol Biol 381 1098 1105 10.1016/j.jmb.2008.06.078 18625239 10.1016/j.jmb.2008.06.078 1:CAS:528:DC%2BD1cXps1Gqurk%3D
-
(2008)
J Mol Biol
, vol.381
, pp. 1098-1105
-
-
Meier, C.1
-
26
-
-
0029047063
-
The adenylate kinases from a mesophilic and three thermophilic methanogenic members of the Archaea
-
7768791 1:CAS:528:DyaK2MXlvFeku7w%3D
-
P Rusnak P Haney J Konisky 1995 The adenylate kinases from a mesophilic and three thermophilic methanogenic members of the Archaea J Bacteriol 177 2977 2981 7768791 1:CAS:528:DyaK2MXlvFeku7w%3D
-
(1995)
J Bacteriol
, vol.177
, pp. 2977-2981
-
-
Rusnak, P.1
Haney, P.2
Konisky, J.3
-
27
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
3447015 1:STN:280:DyaL1c7ovFSjsA%3D%3D
-
N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425 3447015 1:STN:280:DyaL1c7ovFSjsA%3D%3D
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
28
-
-
78651330012
-
BRENDA, the enzyme information system in 2011
-
10.1093/nar/gkq1089 21062828 10.1093/nar/gkq1089
-
M Scheer, et al. 2011 BRENDA, the enzyme information system in 2011 Nucleic Acids Res 39 D670 D676 10.1093/nar/gkq1089 21062828 10.1093/nar/gkq1089
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Scheer, M.1
-
29
-
-
0000398122
-
An iso-random Bi Bi mechanism for adenylate kinase
-
DOI 10.1074/jbc.274.32.22238
-
XR Sheng X Li XM Pan 1999 An iso-random Bi Bi mechanism for adenylate kinase J Biol Chem 274 22238 22242 10428790 10.1074/jbc.274.32.22238 1:CAS:528:DyaK1MXlt1Cgurg%3D (Pubitemid 29379255)
-
(1999)
Journal of Biological Chemistry
, vol.274
, Issue.32
, pp. 22238-22242
-
-
Sheng, X.R.1
Li, X.2
Pan, X.M.3
-
30
-
-
0028279385
-
The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites
-
DOI 10.1111/j.1432-1033.1994.tb18835.x
-
TW Traut 1994 The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites Eur J Biochem 222 9 19 8200357 10.1111/j.1432-1033.1994.tb18835.x 1:CAS:528:DyaK2cXktVajtrY%3D (Pubitemid 24161319)
-
(1994)
European Journal of Biochemistry
, vol.222
, Issue.1
, pp. 9-19
-
-
Traut, T.W.1
-
31
-
-
0027404845
-
Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus
-
DOI 10.1021/bi00054a003
-
RH White 1993 Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus Biochemistry 32 745 753 8422380 10.1021/bi00054a003 1:CAS:528:DyaK3sXlsFOlsA%3D%3D (Pubitemid 23059353)
-
(1993)
Biochemistry
, vol.32
, Issue.3
, pp. 745-753
-
-
White, R.H.1
-
32
-
-
33646591220
-
The difficult road from sequence to function
-
DOI 10.1128/JB.188.10.3431-3432.2006
-
RH White 2006 The difficult road from sequence to function J Bacteriol 188 3431 3432 10.1128/JB.188.10.3431-3432.2006 16672595 10.1128/JB.188.10.3431- 3432.2006 1:CAS:528:DC%2BD28XkslCltLc%3D (Pubitemid 43726205)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.10
, pp. 3431-3432
-
-
White, R.H.1
-
33
-
-
68849088492
-
Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis
-
10.1186/1471-2180-9-149 19627604 10.1186/1471-2180-9-149
-
Q Xia T Wang EL Hendrickson TJ Lie M Hackett JA Leigh 2009 Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis BMC Microbiol 9 149 10.1186/1471-2180-9-149 19627604 10.1186/1471-2180-9-149
-
(2009)
BMC Microbiol
, vol.9
, pp. 149
-
-
Xia, Q.1
Wang, T.2
Hendrickson, E.L.3
Lie, T.J.4
Hackett, M.5
Leigh, J.A.6
-
34
-
-
4444282445
-
Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis
-
DOI 10.1021/pr034109s
-
W Zhu CI Reich GJ Olsen CS Giometti JR Yates 3rd 2004 Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis J Proteome Res 3 538 548 15253435 10.1021/pr034109s 1:CAS:528:DC%2BD2cXisFyitr4%3D (Pubitemid 39207358)
-
(2004)
Journal of Proteome Research
, vol.3
, Issue.3
, pp. 538-548
-
-
Zhu, W.1
Reich, C.I.2
Olsen, G.J.3
Giometti, C.S.4
Yates III, J.R.5
-
35
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
V. Bryson H.J. Vogel (eds). Academic Press New York
-
Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97-166
-
(1965)
Evolving Genes and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
|