-
1
-
-
0035826622
-
Insight into the catalytic mechanism of DNA polymerase beta: Structures of intermediate complex
-
Arndt, J.W., Gong, W., Zhong, X., Showalter, A.K., Liu, J., Dunlap, C.A., Lin, Z., Paxson, C., Tsai, M.D., and Chan, M.K. 2001. Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complex. Biochemistry 40: 5368-5375.
-
(2001)
Biochemistry
, vol.40
, pp. 5368-5375
-
-
Arndt, J.W.1
Gong, W.2
Zhong, X.3
Showalter, A.K.4
Liu, J.5
Dunlap, C.A.6
Lin, Z.7
Paxson, C.8
Tsai, M.D.9
Chan, M.K.10
-
2
-
-
0030667789
-
Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities
-
Babbitt, P.C. and Gerlt, J.A. 1997. Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272: 30591-30594.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 30591-30594
-
-
Babbitt, P.C.1
Gerlt, J.A.2
-
3
-
-
0003717374
-
-
W.H. Freeman and Co., New York
-
Berg, J.M., Tymoczko, J.L., and Stryer, L. 2001. Biochemistry. W.H. Freeman and Co., New York.
-
(2001)
Biochemistry
-
-
Berg, J.M.1
Tymoczko, J.L.2
Stryer, L.3
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
5
-
-
0030927105
-
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli
-
Bertrand, J.A., Auger, G., Fanchon, E., Martin, L., Blanot, D., van Heijenoort, J., and Dideberg, O. 1997. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. EMBO J. 16: 3416-3425.
-
(1997)
EMBO J.
, vol.16
, pp. 3416-3425
-
-
Bertrand, J.A.1
Auger, G.2
Fanchon, E.3
Martin, L.4
Blanot, D.5
Van Heijenoort, J.6
Dideberg, O.7
-
7
-
-
0029619266
-
Molecular evolution of the hisfidine biosynthetic pathway
-
Fani, R., Lio, P., and Lazcano, A. 1995. Molecular evolution of the hisfidine biosynthetic pathway. J. Mol. Evol. 41: 760-774.
-
(1995)
J. Mol. Evol.
, vol.41
, pp. 760-774
-
-
Fani, R.1
Lio, P.2
Lazcano, A.3
-
8
-
-
0025284257
-
The evolution of α/β barrel enzymes
-
Farber, G.K. and Petsko, G.A. 1990. The evolution of α/β barrel enzymes. Trends Biochem. Sci. 15: 228-234.
-
(1990)
Trends Biochem. Sci.
, vol.15
, pp. 228-234
-
-
Farber, G.K.1
Petsko, G.A.2
-
9
-
-
0032483312
-
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
-
Fetrow, J.S. and Skolnick, J. 1998. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281: 949-968.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 949-968
-
-
Fetrow, J.S.1
Skolnick, J.2
-
10
-
-
0028181017
-
An algorithm for automatically generating protein topology cartoons
-
Flores, T.P., Moss, D.S., and Thornton, J.M. 1994. An algorithm for automatically generating protein topology cartoons. Protein Eng. 7: 31-37.
-
(1994)
Protein Eng.
, vol.7
, pp. 31-37
-
-
Flores, T.P.1
Moss, D.S.2
Thornton, J.M.3
-
11
-
-
0033548125
-
Domain dislocation: A change of core structure in periplasmic binding proteins in their evolutionary history
-
Fukami-Kobayashi, K., Tateno, Y., and Nishikawa, K. 1999. Domain dislocation: A change of core structure in periplasmic binding proteins in their evolutionary history. J. Mol. Biol. 286: 279-290.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 279-290
-
-
Fukami-Kobayashi, K.1
Tateno, Y.2
Nishikawa, K.3
-
12
-
-
0032176603
-
Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis
-
Gerlt, J.A. and Babbitt, P.C. 1998. Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis. Curr. Opin. Chem. Biol. 2: 607-612.
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 607-612
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
13
-
-
0035916242
-
The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition
-
Gill, H.S. and Eisenberg, D. 2001. The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition. Biochemistry 40: 1903-1912.
-
(2001)
Biochemistry
, vol.40
, pp. 1903-1912
-
-
Gill, H.S.1
Eisenberg, D.2
-
14
-
-
0033983842
-
LIGAND: Chemical database of enzyme reactions
-
Goto, S., Nishioka, T., and Kanehisa, M. 2000. LIGAND: Chemical database of enzyme reactions. Nucleic Acids Res. 28: 380-382.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 380-382
-
-
Goto, S.1
Nishioka, T.2
Kanehisa, M.3
-
15
-
-
13144255697
-
Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase
-
Hasson, M.S., Schlichting, I., Moulai, L., Taylor, K., Barrett, W., Kenyon, G.L., Babbitt, P.C., Gerlt, J.A., Petsko, G.A., and Ringe, D. 1998. Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proc. Natl. Acad. Sci. 95: 10396-10401.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 10396-10401
-
-
Hasson, M.S.1
Schlichting, I.2
Moulai, L.3
Taylor, K.4
Barrett, W.5
Kenyon, G.L.6
Babbitt, P.C.7
Gerlt, J.A.8
Petsko, G.A.9
Ringe, D.10
-
16
-
-
0030792253
-
SCOP: A structural classification of proteins database
-
Hubbard, T.P.J., Murzin, A.G., Brenner, S.E., and Chothia, C. 1997. SCOP: A structural classification of proteins database. Nucleic Acids Res. 25: 236-239.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 236-239
-
-
Hubbard, T.P.J.1
Murzin, A.G.2
Brenner, S.E.3
Chothia, C.4
-
17
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
18
-
-
0032521456
-
The structure of SAICAR synthase: An enzyme in the de novo pathway of purine nucleotide biosynthesis
-
Levdikov, V.M., Barynin, V.V., Grebenko, A.I., Melik-Adamyan, W.R., Lamzin, V.S., and Wilson, K.S. 1998. The structure of SAICAR synthase: An enzyme in the de novo pathway of purine nucleotide biosynthesis. Structure 6: 363-376.
-
(1998)
Structure
, vol.6
, pp. 363-376
-
-
Levdikov, V.M.1
Barynin, V.V.2
Grebenko, A.I.3
Melik-Adamyan, W.R.4
Lamzin, V.S.5
Wilson, K.S.6
-
19
-
-
0001007592
-
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution
-
Li, C., Kappock, T.J., Stubbe, J.A., Weaver, T.M., and Ealick, S.E. 1999. X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution. Structure 7: 1155-1166.
-
(1999)
Structure
, vol.7
, pp. 1155-1166
-
-
Li, C.1
Kappock, T.J.2
Stubbe, J.A.3
Weaver, T.M.4
Ealick, S.E.5
-
20
-
-
0033977962
-
SCOP: A structural classification of proteins database
-
Lo Conte, L., Ailey, B., Hubbard, T.J.P., Brenner, S.E., Murzin, A.G., and Chothia, C. 2000. SCOP: A structural classification of proteins database. Nucleic Acids Res. 28: 257-259.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 257-259
-
-
Lo Conte, L.1
Ailey, B.2
Hubbard, T.J.P.3
Brenner, S.E.4
Murzin, A.G.5
Chothia, C.6
-
21
-
-
0028593509
-
Protein superfamilies and domain superfolds
-
Orengo, C.A., Jones, D.T., and Thornton, J.M. 1994. Protein superfamilies and domain superfolds. Nature 372: 631-634.
-
(1994)
Nature
, vol.372
, pp. 631-634
-
-
Orengo, C.A.1
Jones, D.T.2
Thornton, J.M.3
-
22
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
23
-
-
0027487948
-
On the origin of enzymatic species
-
Petsko, G.A., Kenyon, G.L., Gerlt, J.A., Ringe, D., and Kozarich, J. W. 1993. On the origin of enzymatic species. Trends Biochem. Sci. 18: 372-376.
-
(1993)
Trends Biochem. Sci.
, vol.18
, pp. 372-376
-
-
Petsko, G.A.1
Kenyon, G.L.2
Gerlt, J.A.3
Ringe, D.4
Kozarich, J.W.5
-
24
-
-
0019053499
-
Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding?
-
Ptitsyn, O.B. and Finkelstein, A.V. 1980. Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding? Q. Rev. Biophysics 13: 339-386.
-
(1980)
Q. Rev. Biophysics
, vol.13
, pp. 339-386
-
-
Ptitsyn, O.B.1
Finkelstein, A.V.2
-
25
-
-
0017387723
-
β-sheet topology and the relatedness of proteins
-
Richardson, J.S. 1977. β-Sheet topology and the relatedness of proteins. Nature 268: 495-500.
-
(1977)
Nature
, vol.268
, pp. 495-500
-
-
Richardson, J.S.1
-
26
-
-
0025048136
-
The P-loop: A common motif in ATP- and GTP-binding proteins
-
Saraste, M., Sibbald, P.R., and Wittinghofer, A. 1990. The P-loop: A common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15: 430-434.
-
(1990)
Trends Biochem. Sci.
, vol.15
, pp. 430-434
-
-
Saraste, M.1
Sibbald, P.R.2
Wittinghofer, A.3
-
27
-
-
0030930760
-
Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J., and Pelletier, H. 1997. Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36: 11205-11215.
-
(1997)
Biochemistry
, vol.36
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, R.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
-
28
-
-
0033598666
-
Three-dimensional structure of N 5-carboxyaminoimidazole ribonucleotide synthetase: A member of the ATP grasp protein superfamily
-
Thoden, J.B., Kappock, T.J., Stubbe, J., and Holden, H.M. 1999. Three-dimensional structure of N 5-carboxyaminoimidazole ribonucleotide synthetase: A member of the ATP grasp protein superfamily. Biochemistry 38: 15480-15492.
-
(1999)
Biochemistry
, vol.38
, pp. 15480-15492
-
-
Thoden, J.B.1
Kappock, T.J.2
Stubbe, J.3
Holden, H.M.4
-
29
-
-
0034254211
-
Molecular structure of Escherichia coli purt-encoded glycinamide ribonucleotide transformylase
-
Thoden, J.B., Firestine, S., Nixon, A., Benkovic, S.J., and Holden, H.M. 2000. Molecular structure of Escherichia coli purt-encoded glycinamide ribonucleotide transformylase. Biochemistry 39: 8791-8802.
-
(2000)
Biochemistry
, vol.39
, pp. 8791-8802
-
-
Thoden, J.B.1
Firestine, S.2
Nixon, A.3
Benkovic, S.J.4
Holden, H.M.5
-
30
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
31
-
-
0004146045
-
-
John Wiley & Sons, New York
-
Voet, D., Voet, J.G., and Pratt, C.W. 1999. Fundamentals of biochemistry. John Wiley & Sons, New York.
-
(1999)
Fundamentals of Biochemistry
-
-
Voet, D.1
Voet, J.G.2
Pratt, C.W.3
-
32
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace, A.C., Laskowski, R.A., and Thornton, J.M. 1995. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8: 127-134.
-
(1995)
Protein Eng.
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
33
-
-
0141827370
-
Derivation of three-dimensional coordinate templates for searching structural databases
-
-. 1996. Derivation of three-dimensional coordinate templates for searching structural databases. Protein Sci. 5: 1001-1013.
-
(1996)
Protein Sci.
, vol.5
, pp. 1001-1013
-
-
-
35
-
-
0032506054
-
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli
-
Wang, W., Kappock, T.J., Stubbe, J., and Ealick, S.E. 1998. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Biochemistry 37: 15647-15652.
-
(1998)
Biochemistry
, vol.37
, pp. 15647-15652
-
-
Wang, W.1
Kappock, T.J.2
Stubbe, J.3
Ealick, S.E.4
|