-
1
-
-
0028918401
-
A proficient enzyme
-
Radzicka, A., and Wolfenden, R. (1995) A proficient enzyme. Science 267, 90-93
-
(1995)
Science
, vol.267
, pp. 90-93
-
-
Radzicka, A.1
Wolfenden, R.2
-
2
-
-
0034058368
-
The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase
-
Appleby, T. C., Kinsland, C., Begley, T. P., and Ealick, S. E. (2000) The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase. Proc. Natl. Acad. Sci. U.S.A. 97, 2005-2010
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 2005-2010
-
-
Appleby, T.C.1
Kinsland, C.2
Begley, T.P.3
Ealick, S.E.4
-
3
-
-
0034681950
-
Structural basis for the catalytic mechanism of a proficient enzyme: Orotidine 5′-monophosphate decarboxylase
-
Harris, P., Navarro Poulsen, J. C., Jensen, K. F., and Larsen, S. (2000) Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5′-monophosphate decarboxylase. Biochemistry 39, 4217-4224
-
(2000)
Biochemistry
, vol.39
, pp. 4217-4224
-
-
Harris, P.1
Navarro Poulsen, J.C.2
Jensen, K.F.3
Larsen, S.4
-
4
-
-
0034104285
-
Anatomy of a proficient enzyme: The structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog
-
Miller, B. G., Hassell, A. M., Wolfenden, R., Milburn, M. V., and Short, S. A. (2000) Anatomy of a proficient enzyme: the structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog. Proc. Natl. Acad. Sci. U.S.A. 97, 2011-2016
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 2011-2016
-
-
Miller, B.G.1
Hassell, A.M.2
Wolfenden, R.3
Milburn, M.V.4
Short, S.A.5
-
5
-
-
0034102419
-
Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase
-
Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 2017-2022
-
-
Wu, N.1
Mo, Y.2
Gao, J.3
Pai, E.F.4
-
6
-
-
38949172353
-
Formation and stability of a vinyl carbanion at the active site of orotidine 5′-monophosphate decarboxylase: PKa of the C-6 proton of enzymebound UMP
-
Amyes, T. L., Wood, B. M., Chan, K., Gerlt, J. A., and Richard, J. P. (2008) Formation and stability of a vinyl carbanion at the active site of orotidine 5′-monophosphate decarboxylase: pKa of the C-6 proton of enzymebound UMP. J. Am. Chem. Soc. 130, 1574-1575
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 1574-1575
-
-
Amyes, T.L.1
Wood, B.M.2
Chan, K.3
Gerlt, J.A.4
Richard, J.P.5
-
7
-
-
77952556805
-
Product deuterium isotope effects for orotidine 5′-monophosphate decarboxylase: Effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate
-
Toth, K., Amyes, T. L., Wood, B. M., Chan, K., Gerlt, J. A., and Richard, J. P. (2010) Product deuterium isotope effects for orotidine 5′-monophosphate decarboxylase: effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate. J. Am. Chem. Soc. 132, 7018-7024
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 7018-7024
-
-
Toth, K.1
Amyes, T.L.2
Wood, B.M.3
Chan, K.4
Gerlt, J.A.5
Richard, J.P.6
-
8
-
-
27544496503
-
An unprecedented twist to ODCase catalytic activity
-
Fujihashi, M., Bello, A. M., Poduch, E., Wei, L., Annedi, S. C., Pai, E. F., and Kotra, L. P. (2005) An unprecedented twist to ODCase catalytic activity. J. Am. Chem. Soc. 127, 15048-15050
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 15048-15050
-
-
Fujihashi, M.1
Bello, A.M.2
Poduch, E.3
Wei, L.4
Annedi, S.C.5
Pai, E.F.6
Kotra, L.P.7
-
9
-
-
67649210974
-
Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Evidence for substrate destabilization
-
Chan, K. K., Wood, B. M., Fedorov, A. A., Fedorov, E. V., Imker, H. J., Amyes, T. L., Richard, J. P., Almo, S. C., and Gerlt, J. A. (2009) Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Biochemistry 48, 5518-5531
-
(2009)
Biochemistry
, vol.48
, pp. 5518-5531
-
-
Chan, K.K.1
Wood, B.M.2
Fedorov, A.A.3
Fedorov, E.V.4
Imker, H.J.5
Amyes, T.L.6
Richard, J.P.7
Almo, S.C.8
Gerlt, J.A.9
-
10
-
-
0037396515
-
Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase
-
Gao, J. (2003) Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase. Curr. Opin. Struct. Biol. 13, 184-192
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 184-192
-
-
Gao, J.1
-
11
-
-
0037177230
-
Mapping the active site-ligand interactions of orotidine 5′-monophosphate decarboxylase by crystallography
-
Wu, N., Gillon, W., and Pai, E. F. (2002) Mapping the active site-ligand interactions of orotidine 5′-monophosphate decarboxylase by crystallography. Biochemistry 41, 4002-4011
-
(2002)
Biochemistry
, vol.41
, pp. 4002-4011
-
-
Wu, N.1
Gillon, W.2
Pai, E.F.3
-
12
-
-
37549059177
-
Structures of the human orotidine-5′-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
-
Wittmann, J. G., Heinrich, D., Gasow, K., Frey, A., Diederichsen, U., and Rudolph, M. G. (2008) Structures of the human orotidine-5′-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Structure 16, 82-92
-
(2008)
Structure
, vol.16
, pp. 82-92
-
-
Wittmann, J.G.1
Heinrich, D.2
Gasow, K.3
Frey, A.4
Diederichsen, U.5
Rudolph, M.G.6
-
13
-
-
67649642022
-
Lys314 is a nucleophile in non-classical reactions of orotidine-5′-monophosphate decarboxylase
-
Heinrich, D., Diederichsen, U., and Rudolph, M. G. (2009) Lys314 is a nucleophile in non-classical reactions of orotidine-5′-monophosphate decarboxylase. Chemistry 15, 6619-6625
-
(2009)
Chemistry
, vol.15
, pp. 6619-6625
-
-
Heinrich, D.1
Diederichsen, U.2
Rudolph, M.G.3
-
14
-
-
63649145250
-
Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5′-monophosphate decarboxylase
-
Fujihashi, M., Wei, L., Kotra, L. P., and Pai, E. F. (2009) Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5′-monophosphate decarboxylase. J. Mol. Biol. 387, 1199-1210
-
(2009)
J. Mol. Biol.
, vol.387
, pp. 1199-1210
-
-
Fujihashi, M.1
Wei, L.2
Kotra, L.P.3
Pai, E.F.4
-
15
-
-
33644936395
-
ARamanactive competitive inhibitor of OMP decarboxylase
-
Callahan, B. P., Bell, A. F., Tonge, P. J., and Wolfenden, R. (2006)ARamanactive competitive inhibitor of OMP decarboxylase. Bioorg. Chem. 34, 59-65
-
(2006)
Bioorg. Chem.
, vol.34
, pp. 59-65
-
-
Callahan, B.P.1
Bell, A.F.2
Tonge, P.J.3
Wolfenden, R.4
-
16
-
-
37549009025
-
Structural basis for the decarboxylation of orotidine 5′-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase
-
Tokuoka, K., Kusakari, Y., Krungkrai, S. R., Matsumura, H., Kai, Y., Krungkrai, J., Horii, T., and Inoue, T. (2008) Structural basis for the decarboxylation of orotidine 5′-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase. J. Biochem. 143, 69-78
-
(2008)
J. Biochem.
, vol.143
, pp. 69-78
-
-
Tokuoka, K.1
Kusakari, Y.2
Krungkrai, S.R.3
Matsumura, H.4
Kai, Y.5
Krungkrai, J.6
Horii, T.7
Inoue, T.8
-
17
-
-
13444273194
-
A novel enzyme complex of orotate phosphoribosyltransferase and orotidine 5′-monophosphate decarboxylase in human malaria parasite Plasmodium falciparum: Physical association, kinetics, and inhibition characterization
-
Krungkrai, S. R., DelFraino, B. J., Smiley, J. A., Prapunwattana, P., Mitamura, T., Horii, T., and Krungkrai, J. (2005) A novel enzyme complex of orotate phosphoribosyltransferase and orotidine 5′-monophosphate decarboxylase in human malaria parasite Plasmodium falciparum: physical association, kinetics, and inhibition characterization. Biochemistry 44, 1643-1652
-
(2005)
Biochemistry
, vol.44
, pp. 1643-1652
-
-
Krungkrai, S.R.1
Delfraino, B.J.2
Smiley, J.A.3
Prapunwattana, P.4
Mitamura, T.5
Horii, T.6
Krungkrai, J.7
-
18
-
-
36249011948
-
Indiscriminate binding by orotidine 5′-phosphate decarboxylase of uridine 5′-phosphate derivatives with bulky anionic c6 substituents
-
Lewis, C. A., Jr., and Wolfenden, R. (2007) Indiscriminate binding by orotidine 5′-phosphate decarboxylase of uridine 5′-phosphate derivatives with bulky anionic c6 substituents. Biochemistry 46, 13331-13343
-
(2007)
Biochemistry
, vol.46
, pp. 13331-13343
-
-
Lewis Jr., C.A.1
Wolfenden, R.2
-
19
-
-
0034013743
-
Crystallization of native and selenomethionyl yeast orotidine 5′-phosphate decarboxylase
-
Miller, B. G., Hassell, A. M., Milburn, M. V., and Short, S. A. (2000) Crystallization of native and selenomethionyl yeast orotidine 5′-phosphate decarboxylase. Acta Crystallogr. D Biol. Crystallogr. 56, 472-474
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 472-474
-
-
Miller, B.G.1
Hassell, A.M.2
Milburn, M.V.3
Short, S.A.4
-
20
-
-
39149127980
-
Structural diversity and plasticity associated with nucleotides targeting orotidine monophosphate decarboxylase
-
Poduch, E., Wei, L., Pai, E. F., and Kotra, L. P. (2008) Structural diversity and plasticity associated with nucleotides targeting orotidine monophosphate decarboxylase. J. Med. Chem. 51, 432-438
-
(2008)
J. Med. Chem.
, vol.51
, pp. 432-438
-
-
Poduch, E.1
Wei, L.2
Pai, E.F.3
Kotra, L.P.4
-
21
-
-
77957157501
-
On catalytic preorganization in oxyanion holes: Highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models
-
Kamerlin, S. C., Chu, Z. T., and Warshel, A. (2010) On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models. J. Org. Chem. 75, 6391-6401
-
(2010)
J. Org. Chem.
, vol.75
, pp. 6391-6401
-
-
Kamerlin, S.C.1
Chu, Z.T.2
Warshel, A.3
-
22
-
-
0033937431
-
Purification, crystallization, and preliminary X-ray study of orotidine 5′-monophosphate decarboxylase
-
Wu, N., Christendat, D., Dharamsi, A., and Pai, E. F. (2000) Purification, crystallization, and preliminary X-ray study of orotidine 5′-monophosphate decarboxylase. Acta Crystallogr. D Biol. Crystallogr. 56, 912-914
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 912-914
-
-
Wu, N.1
Christendat, D.2
Dharamsi, A.3
Pai, E.F.4
-
23
-
-
0031059866
-
Processing of x-ray diffraction data collected in oscillation mode
-
Otwinowski, Z., and Minor, W. (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
-
(1997)
Methods Enzymol
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
25
-
-
0032897075
-
Efficient anisotropic refinement of macromolecular structures using FFT
-
Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S., and Dodson, E. J. (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D Biol. Crystallogr. 55, 247-255
-
(1999)
Acta Crystallogr. D Biol. Crystallogr.
, vol.55
, pp. 247-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Lebedev, A.3
Wilson, K.S.4
Dodson, E.J.5
-
26
-
-
37549039510
-
A short history of SHELX
-
Sheldrick, G. M. (2008) A short history of SHELX. Acta Crystallogr. A 64, 112-122
-
(2008)
Acta Crystallogr. A
, vol.64
, pp. 112-122
-
-
Sheldrick, G.M.1
-
27
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen, V. B., Arendall, W. B., 3rd, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., and Richardson, D. C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall III, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
28
-
-
37049079283
-
Anovel hydrogel matrix on gold surfaces in surface-plasmon resonance sensors for fast and efficient covalent immobilization of ligands
-
Lofas, S., and Johnsson, B. (1990)Anovel hydrogel matrix on gold surfaces in surface-plasmon resonance sensors for fast and efficient covalent immobilization of ligands. J. Chem. Soc. Chem. Commun. 1526-1528
-
(1990)
J. Chem. Soc. Chem. Commun.
, pp. 1526-1528
-
-
Lofas, S.1
Johnsson, B.2
-
29
-
-
0037008729
-
Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5′-monophosphate decarboxylase
-
Wu, N., and Pai, E. F. (2002) Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5′-monophosphate decarboxylase. J. Biol. Chem. 277, 28080-28087
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 28080-28087
-
-
Wu, N.1
Pai, E.F.2
-
30
-
-
0035967499
-
Role of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5′-phosphate decarboxylase: A role for substrate destabilization?
-
Miller, B. G., Butterfoss, G. L., Short, S. A., and Wolfenden, R. (2001) Role of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5′-phosphate decarboxylase: a role for substrate destabilization? Biochemistry 40, 6227-6232
-
(2001)
Biochemistry
, vol.40
, pp. 6227-6232
-
-
Miller, B.G.1
Butterfoss, G.L.2
Short, S.A.3
Wolfenden, R.4
-
31
-
-
64349090835
-
Structure-activity relationships of orotidine-5′-monophosphate decarboxylase inhibitors as anticancer agents
-
Bello, A. M., Konforte, D., Poduch, E., Furlonger, C., Wei, L., Liu, Y., Lewis, M., Pai, E. F., Paige, C. J., and Kotra, L. P. (2009) Structure-activity relationships of orotidine-5′-monophosphate decarboxylase inhibitors as anticancer agents. J. Med. Chem. 52, 1648-1658
-
(2009)
J. Med. Chem.
, vol.52
, pp. 1648-1658
-
-
Bello, A.M.1
Konforte, D.2
Poduch, E.3
Furlonger, C.4
Wei, L.5
Liu, Y.6
Lewis, M.7
Pai, E.F.8
Paige, C.J.9
Kotra, L.P.10
-
32
-
-
39149112528
-
Structure-activity relationships of C6-uridine derivatives targeting plasmodia orotidine monophosphate decarboxylase
-
Bello, A. M., Poduch, E., Liu, Y., Wei, L., Crandall, I., Wang, X., Dyanand, C., Kain, K. C., Pai, E. F., and Kotra, L. P. (2008) Structure-activity relationships of C6-uridine derivatives targeting plasmodia orotidine monophosphate decarboxylase. J. Med. Chem. 51, 439-448
-
(2008)
J. Med. Chem.
, vol.51
, pp. 439-448
-
-
Bello, A.M.1
Poduch, E.2
Liu, Y.3
Wei, L.4
Crandall, I.5
Wang, X.6
Dyanand, C.7
Kain, K.C.8
Pai, E.F.9
Kotra, L.P.10
-
33
-
-
79955405438
-
Novel interactions of fluorinated nucleotide derivatives targeting orotidine 5′- monophosphate decarboxylase
-
Lewis, M., Meza-Avina, M. E., Wei, L., Crandall, I. E., Bello, A. M., Poduch, E., Liu, Y., Paige, C. J., Kain, K. C., Pai, E. F., and Kotra, L. P. (2011) Novel interactions of fluorinated nucleotide derivatives targeting orotidine 5′- monophosphate decarboxylase. J. Med. Chem. 54, 2891-2901
-
(2011)
J. Med. Chem.
, vol.54
, pp. 2891-2901
-
-
Lewis, M.1
Meza-Avina, M.E.2
Wei, L.3
Crandall, I.E.4
Bello, A.M.5
Poduch, E.6
Liu, Y.7
Paige, C.J.8
Kain, K.C.9
Pai, E.F.10
Kotra, L.P.11
-
34
-
-
77953139557
-
Structural determinants for the inhibitory ligands of orotidine-5′-monophosphate decarboxylase
-
Meza-Avina, M. E., Wei, L., Liu, Y., Poduch, E., Bello, A. M., Mishra, R. K., Pai, E. F., and Kotra, L. P. (2010) Structural determinants for the inhibitory ligands of orotidine-5′-monophosphate decarboxylase. Bioorg. Med. Chem. 18, 4032-4041
-
(2010)
Bioorg. Med. Chem.
, vol.18
, pp. 4032-4041
-
-
Meza-Avina, M.E.1
Wei, L.2
Liu, Y.3
Poduch, E.4
Bello, A.M.5
Mishra, R.K.6
Pai, E.F.7
Kotra, L.P.8
-
35
-
-
33746911969
-
Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics
-
Poduch, E., Bello, A. M., Tang, S., Fujihashi, M., Pai, E. F., and Kotra, L. P. (2006) Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics. J. Med. Chem. 49, 4937-4945
-
(2006)
J. Med. Chem.
, vol.49
, pp. 4937-4945
-
-
Poduch, E.1
Bello, A.M.2
Tang, S.3
Fujihashi, M.4
Pai, E.F.5
Kotra, L.P.6
-
36
-
-
77951808779
-
Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6
-
Thirumalairajan, S., Mahaney, B., and Bearne, S. L. (2010) Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6. Chem. Commun. (Camb.) 46, 3158-3160
-
(2010)
Chem. Commun. (Camb.)
, vol.46
, pp. 3158-3160
-
-
Thirumalairajan, S.1
Mahaney, B.2
Bearne, S.L.3
-
37
-
-
84862196265
-
Orotidine 5′-monophosphate decarboxylase: Transition state stabilization from remote protein-phosphodianion interactions
-
Amyes, T. L., Ming, S. A., Goldman, L. M., Wood, B. M., Desai, B. J., Gerlt, J. A., and Richard, J. P. (2012) Orotidine 5′-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions. Biochemistry 51, 4630-4632
-
(2012)
Biochemistry
, vol.51
, pp. 4630-4632
-
-
Amyes, T.L.1
Ming, S.A.2
Goldman, L.M.3
Wood, B.M.4
Desai, B.J.5
Gerlt, J.A.6
Richard, J.P.7
-
38
-
-
84868089459
-
Conformational changes in orotidine 5′-monophosphate decarboxylase: A structure- based explanation for how the 5′-phosphate group activates the enzyme
-
Desai, B. J., Wood, B. M., Fedorov, A. A., Fedorov, E. V., Goryanova, B., Amyes, T. L., Richard, J. P., Almo, S. C., and Gerlt, J. A. (2012) Conformational changes in orotidine 5′-monophosphate decarboxylase: a structure- based explanation for how the 5′-phosphate group activates the enzyme. Biochemistry 51, 8665-8678
-
(2012)
Biochemistry
, vol.51
, pp. 8665-8678
-
-
Desai, B.J.1
Wood, B.M.2
Fedorov, A.A.3
Fedorov, E.V.4
Goryanova, B.5
Amyes, T.L.6
Richard, J.P.7
Almo, S.C.8
Gerlt, J.A.9
-
39
-
-
0035788131
-
Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps
-
Vagin, A. A., and Isupov, M. N. (2001) Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps. Acta Crystallogr. D Biol. Crystallogr. 57, 1451-1456
-
(2001)
Acta Crystallogr. D Biol. Crystallogr.
, vol.57
, pp. 1451-1456
-
-
Vagin, A.A.1
Isupov, M.N.2
|