-
1
-
-
77954762555
-
Occurrence, biosynthesis and function of isoprenoid quinones
-
Nowicka B, Kruk J, (2010) Occurrence, biosynthesis and function of isoprenoid quinones. Biochimica et biophysica acta 1797: 1587-1605.
-
(2010)
Biochimica Et Biophysica Acta
, vol.1797
, pp. 1587-1605
-
-
Nowicka, B.1
Kruk, J.2
-
2
-
-
0035219809
-
Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms
-
Meganathan R, (2001) Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms. Vitamins and Hormones 61: 173-218.
-
(2001)
Vitamins and Hormones
, vol.61
, pp. 173-218
-
-
Meganathan, R.1
-
3
-
-
84865978841
-
On the function of the various quinone species in Escherichia coli
-
Sharma P, Teixeira de Mattos MJ, Hellingwerf KJ, Bekker M, (2012) On the function of the various quinone species in Escherichia coli. The FEBS journal 279(18): 3364-3373.
-
(2012)
The FEBS Journal
, vol.279
, Issue.18
, pp. 3364-3373
-
-
Sharma, P.1
Teixeira de Mattos, M.J.2
Hellingwerf, K.J.3
Bekker, M.4
-
4
-
-
62949112206
-
Menaquinone synthesis is critical for maintaining mycobacterial viability during exponential growth and recovery from non-replicating persistence
-
Dhiman RK, Mahapatra S, Slayden RA, Boyne ME, Lenaerts A, et al. (2009) Menaquinone synthesis is critical for maintaining mycobacterial viability during exponential growth and recovery from non-replicating persistence. Mol Microbiol 72: 85-97.
-
(2009)
Mol Microbiol
, vol.72
, pp. 85-97
-
-
Dhiman, R.K.1
Mahapatra, S.2
Slayden, R.A.3
Boyne, M.E.4
Lenaerts, A.5
-
5
-
-
84860308064
-
Discovery of selective menaquinone biosynthesis inhibitors against Mycobacterium tuberculosis
-
Debnath J, Siricilla S, Wan B, Crick DC, Lenaerts AJ, et al. (2012) Discovery of selective menaquinone biosynthesis inhibitors against Mycobacterium tuberculosis. Journal of medicinal chemistry 55: 3739-3755.
-
(2012)
Journal of Medicinal Chemistry
, vol.55
, pp. 3739-3755
-
-
Debnath, J.1
Siricilla, S.2
Wan, B.3
Crick, D.C.4
Lenaerts, A.J.5
-
6
-
-
80052051631
-
Convergent strategies in biosynthesis
-
Dairi T, Kuzuyama T, Nishiyama M, Fujii I, (2011) Convergent strategies in biosynthesis. Natural product reports 28: 1054-1086.
-
(2011)
Natural Product Reports
, vol.28
, pp. 1054-1086
-
-
Dairi, T.1
Kuzuyama, T.2
Nishiyama, M.3
Fujii, I.4
-
7
-
-
52249100797
-
An alternative menaquinone biosynthetic pathway operating in microorganisms
-
Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, et al. (2008) An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321: 1670-1673.
-
(2008)
Science
, vol.321
, pp. 1670-1673
-
-
Hiratsuka, T.1
Furihata, K.2
Ishikawa, J.3
Yamashita, H.4
Itoh, N.5
-
8
-
-
34648813427
-
Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity
-
Jiang M, Cao Y, Guo ZF, Chen M, Chen X, et al. (2007) Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 46: 10979-10989.
-
(2007)
Biochemistry
, vol.46
, pp. 10979-10989
-
-
Jiang, M.1
Cao, Y.2
Guo, Z.F.3
Chen, M.4
Chen, X.5
-
9
-
-
67651208493
-
Catalytic mechanism of SHCHC synthase in the menaquinone biosynthesis of Escherichia coli: identification and mutational analysis of the active site residues
-
Jiang M, Chen X, Wu XH, Chen M, Wu YD, et al. (2009) Catalytic mechanism of SHCHC synthase in the menaquinone biosynthesis of Escherichia coli: identification and mutational analysis of the active site residues. Biochemistry 48: 6921-6931.
-
(2009)
Biochemistry
, vol.48
, pp. 6921-6931
-
-
Jiang, M.1
Chen, X.2
Wu, X.H.3
Chen, M.4
Wu, Y.D.5
-
10
-
-
40849094350
-
Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli
-
Jiang M, Chen X, Guo ZF, Cao Y, Chen M, et al. (2008) Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli. Biochemistry 47: 3426-3434.
-
(2008)
Biochemistry
, vol.47
, pp. 3426-3434
-
-
Jiang, M.1
Chen, X.2
Guo, Z.F.3
Cao, Y.4
Chen, M.5
-
11
-
-
0032784276
-
Alpha/beta hydrolase fold enzymes: the family keeps growing
-
Nardini M, Dijkstra BW, (1999) Alpha/beta hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 9: 732-737.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 732-737
-
-
Nardini, M.1
Dijkstra, B.W.2
-
12
-
-
79955043152
-
Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity
-
Dawson A, Fyfe PK, Gillet F, Hunter WN, (2011) Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity. BMC structural biology 11: 19.
-
(2011)
BMC Structural Biology
, vol.11
, pp. 19
-
-
Dawson, A.1
Fyfe, P.K.2
Gillet, F.3
Hunter, W.N.4
-
13
-
-
14844294424
-
Protein production by auto-induction in high density shaking cultures
-
Studier FW, (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207-234.
-
(2005)
Protein Expr Purif
, vol.41
, pp. 207-234
-
-
Studier, F.W.1
-
14
-
-
32444432412
-
A flexible and economical medium-throughput strategy for protein production and crystallization
-
Moreland N, Ashton R, Baker HM, Ivanovic I, Patterson S, et al. (2005) A flexible and economical medium-throughput strategy for protein production and crystallization. Acta Crystallogr D Biol Crystallogr 61: 1378-1385.
-
(2005)
Acta Crystallogr D Biol Crystallogr
, vol.61
, pp. 1378-1385
-
-
Moreland, N.1
Ashton, R.2
Baker, H.M.3
Ivanovic, I.4
Patterson, S.5
-
15
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology 276: 307-326.
-
(1997)
Methods in Enzymology
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
17
-
-
76449106188
-
Integration, scaling, space-group assignment and post-refinement
-
Kabsch W, (2010) Integration, scaling, space-group assignment and post-refinement. Acta crystallographica Section D, Biological crystallography 66: 133-144.
-
(2010)
Acta Crystallographica Section D, Biological Crystallography
, vol.66
, pp. 133-144
-
-
Kabsch, W.1
-
19
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta crystallographica Section D, Biological crystallography 67: 235-242.
-
(2011)
Acta Crystallographica Section D, Biological Crystallography
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
Ballard, C.C.2
Cowtan, K.D.3
Dodson, E.J.4
Emsley, P.5
-
20
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
-
(2007)
J Appl Crystallogr
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
-
21
-
-
37349023302
-
BALBES: a molecular-replacement pipeline
-
Long F, Vagin AA, Young P, Murshudov GN, (2008) BALBES: a molecular-replacement pipeline. Acta crystallographica Section D, Biological crystallography 64: 125-132.
-
(2008)
Acta Crystallographica Section D, Biological Crystallography
, vol.64
, pp. 125-132
-
-
Long, F.1
Vagin, A.A.2
Young, P.3
Murshudov, G.N.4
-
22
-
-
77949535720
-
Features and development of Coot
-
Emsley P, Lohkamp B, Scott WG, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
23
-
-
79953763877
-
REFMAC5 for the refinement of macromolecular crystal structures
-
Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, et al. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta crystallographica Section D, Biological crystallography 67: 355-367.
-
(2011)
Acta Crystallographica Section D, Biological Crystallography
, vol.67
, pp. 355-367
-
-
Murshudov, G.N.1
Skubak, P.2
Lebedev, A.A.3
Pannu, N.S.4
Steiner, R.A.5
-
24
-
-
77957946297
-
-
Cambridge, United Kingdom Global Phasing Ltd
-
Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P, et al. (2011) BUSTER version 2.10.0. Cambridge, United Kingdom Global Phasing Ltd.
-
(2011)
BUSTER version 2.10.0
-
-
Bricogne, G.1
Blanc, E.2
Brandl, M.3
Flensburg, C.4
Keller, P.5
-
25
-
-
0000560808
-
MOLREP: an automated program for molecular replacement
-
Vagin A, Teplyakov A, (1997) MOLREP: an automated program for molecular replacement. Journal of Applied Crystallography 30: 1022-1025.
-
(1997)
Journal of Applied Crystallography
, vol.30
, pp. 1022-1025
-
-
Vagin, A.1
Teplyakov, A.2
-
26
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta crystallographica Section D, Biological crystallography 66: 12-21.
-
(2010)
Acta Crystallographica Section D, Biological Crystallography
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall 3rd, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
-
27
-
-
0003845223
-
-
San Carlos, CA: DeLano Scientific. Available:. Accessed 2013 Mar 27
-
DeLano WL (2002) The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific. Available: http://www.pymol.org/. Accessed 2013 Mar 27.
-
(2002)
The PyMOL molecular graphics system
-
-
DeLano, W.L.1
-
29
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD, (2003) Improved protein-ligand docking using GOLD. Proteins 52: 609-623.
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
30
-
-
0034663722
-
The penultimate rotamer library
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (2000) The penultimate rotamer library. Proteins 40: 389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
31
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology 372: 774-797.
-
(2007)
Journal of Molecular Biology
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
32
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel E, Henrick K, (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta crystallographica Section D, Biological crystallography 60: 2256-2268.
-
(2004)
Acta Crystallographica Section D, Biological Crystallography
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
33
-
-
0026540411
-
The alpha/beta hydrolase fold
-
Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, et al. (1992) The alpha/beta hydrolase fold. Protein Eng 5: 197-211.
-
(1992)
Protein Eng
, vol.5
, pp. 197-211
-
-
Ollis, D.L.1
Cheah, E.2
Cygler, M.3
Dijkstra, B.4
Frolow, F.5
-
34
-
-
0034285515
-
Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms
-
Holmquist M, (2000) Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms. Curr Protein Pept Sci 1: 209-235.
-
(2000)
Curr Protein Pept Sci
, vol.1
, pp. 209-235
-
-
Holmquist, M.1
-
36
-
-
77955453338
-
Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis
-
Johnston JM, Jiang M, Guo Z, Baker EN, (2010) Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis. Acta crystallographica Section D, Biological crystallography 66: 909-917.
-
(2010)
Acta Crystallographica Section D, Biological Crystallography
, vol.66
, pp. 909-917
-
-
Johnston, J.M.1
Jiang, M.2
Guo, Z.3
Baker, E.N.4
-
37
-
-
33747818007
-
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, et al. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34: W116-118.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
-
38
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
-
39
-
-
0032961270
-
ESPript: analysis of multiple sequence alignments in PostScript
-
Gouet P, Courcelle E, Stuart DI, Metoz F, (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.
-
(1999)
Bioinformatics
, vol.15
, pp. 305-308
-
-
Gouet, P.1
Courcelle, E.2
Stuart, D.I.3
Metoz, F.4
|