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Volumn 7, Issue 1, 2003, Pages 28-32

Overview of structural genomics: From structure to function

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 0037305974     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(02)00015-7     Document Type: Review
Times cited : (125)

References (44)
  • 2
    • 0031928367 scopus 로고    scopus 로고
    • Shining a light on structural genomics
    • Kim S.H. Shining a light on structural genomics. Nature Struct. Biol. 5:1998;643-645.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 643-645
    • Kim, S.H.1
  • 3
    • 0032104477 scopus 로고    scopus 로고
    • How far divergent evolution goes in proteins
    • Murzin A.G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:1998;380-387.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 380-387
    • Murzin, A.G.1
  • 4
    • 0036228122 scopus 로고    scopus 로고
    • Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics
    • Aloy P., Oliva B., Querol E., Aviles F.X., Russell R.B. Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. Protein Sci. 11:2002;1101-1116.
    • (2002) Protein Sci. , vol.11 , pp. 1101-1116
    • Aloy, P.1    Oliva, B.2    Querol, E.3    Aviles, F.X.4    Russell, R.B.5
  • 5
    • 17444398048 scopus 로고    scopus 로고
    • Structure-based identification of a novel NTPase from Methanococcus jannaschii
    • Hwang K.Y., Chung J.H., Kim S.H., Han Y.S., Cho Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat. Struct. Biol. 6:1999;691-696.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 691-696
    • Hwang, K.Y.1    Chung, J.H.2    Kim, S.H.3    Han, Y.S.4    Cho, Y.5
  • 6
    • 0032787396 scopus 로고    scopus 로고
    • Implication of tubby proteins as transcription factors by structure-based functional analysis
    • Boggon T.J., Shan W.S., Santagata S., Myers S.C., Shapiro L. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science. 286:1999;2119-2125.
    • (1999) Science , vol.286 , pp. 2119-2125
    • Boggon, T.J.1    Shan, W.S.2    Santagata, S.3    Myers, S.C.4    Shapiro, L.5
  • 7
    • 0036584359 scopus 로고    scopus 로고
    • Timeline: The march of structural biology
    • Campbell I.D. Timeline: the march of structural biology. Nat. Rev. Mol. Cell Biol. 3:2002;377-381.
    • (2002) Nat. Rev. Mol. Cell Biol. , vol.3 , pp. 377-381
    • Campbell, I.D.1
  • 8
    • 0035812704 scopus 로고    scopus 로고
    • Global efforts in structural genomics
    • Stevens R.C., Yokoyama S., Wilson I.A. Global efforts in structural genomics. Science. 294:2001;89-92.
    • (2001) Science , vol.294 , pp. 89-92
    • Stevens, R.C.1    Yokoyama, S.2    Wilson, I.A.3
  • 9
    • 0033757870 scopus 로고    scopus 로고
    • Structural genomics in North America
    • Terwilliger T.C. Structural genomics in North America. Nat. Struct. Biol. 7:2000;935-939.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 935-939
    • Terwilliger, T.C.1
  • 11
    • 0033757915 scopus 로고    scopus 로고
    • Structural genomics in Europe: Slow start, strong finish?
    • Heinemann U. Structural genomics in Europe: slow start, strong finish? Nat. Struct. Biol. 7:2000;940-942.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 940-942
    • Heinemann, U.1
  • 14
    • 0036075170 scopus 로고    scopus 로고
    • Protein crystallization for genomics: Towards high-throughput optimization techniques
    • Chayen N.E., Saridakis E. Protein crystallization for genomics: towards high-throughput optimization techniques. Acta. Crystallogr. D. 58:2002;921-927.
    • (2002) Acta. Crystallogr. D , vol.58 , pp. 921-927
    • Chayen, N.E.1    Saridakis, E.2
  • 15
    • 0036137978 scopus 로고    scopus 로고
    • Fast drops: A high-throughput approach for setting up protein crystal screens
    • Villaseñor A., Sha M., Thana P., Browner M. Fast drops: a high-throughput approach for setting up protein crystal screens. BioTechniques. 32:2002;184-189.
    • (2002) BioTechniques , vol.32 , pp. 184-189
    • Villaseñor, A.1    Sha, M.2    Thana, P.3    Browner, M.4
  • 16
    • 0036793459 scopus 로고    scopus 로고
    • Automated mounting, centering and screening of crystals for high-throughput protein crystallography
    • Karain W.I., Bourenkov G.P., Blume H., Bartunik H.D. Automated mounting, centering and screening of crystals for high-throughput protein crystallography. Acta. Crystallogr. D. 58:2002;1519-1522.
    • (2002) Acta. Crystallogr. D , vol.58 , pp. 1519-1522
    • Karain, W.I.1    Bourenkov, G.P.2    Blume, H.3    Bartunik, H.D.4
  • 18
    • 0035846574 scopus 로고    scopus 로고
    • An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR
    • Bhavesh N.S., Panchal S.C., Hosur R.V. An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR. Biochemistry. 40:2001;14727-14735.
    • (2001) Biochemistry , vol.40 , pp. 14727-14735
    • Bhavesh, N.S.1    Panchal, S.C.2    Hosur, R.V.3
  • 20
    • 0037015054 scopus 로고    scopus 로고
    • Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
    • This paper describes the high-throughput structural determination pipeline designed and implemented at Syrrx Corp. and the Joint Center for Structural Genomics. The results of the application of the pipeline to the proteome of thermophillic bacterium Thermotaga maritima are presented. Of the two structures used as examples of the final outputs of the pipeline, the structure of thymidylate synthase-complementing protein TM0423 is of particular interest. The presence of four FAD molecules in the central active site of the TM0423 tetramer suggests a flavin-dependent mechanism in the alternative thymidylate synthesis pathway.
    • Lesley S.A., Kuhn P., Godzik A., Deacon A.M., Mathews I., Kreusch A., Spraggon G., Klock H.E., McMullan D., Shin T.et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. U.S.A. 99:2002;11664-11669 This paper describes the high-throughput structural determination pipeline designed and implemented at Syrrx Corp. and the Joint Center for Structural Genomics. The results of the application of the pipeline to the proteome of thermophillic bacterium Thermotaga maritima are presented. Of the two structures used as examples of the final outputs of the pipeline, the structure of thymidylate synthase-complementing protein TM0423 is of particular interest. The presence of four FAD molecules in the central active site of the TM0423 tetramer suggests a flavin-dependent mechanism in the alternative thymidylate synthesis pathway.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 11664-11669
    • Lesley, S.A.1    Kuhn, P.2    Godzik, A.3    Deacon, A.M.4    Mathews, I.5    Kreusch, A.6    Spraggon, G.7    Klock, H.E.8    McMullan, D.9    Shin, T.10
  • 21
    • 0036600569 scopus 로고    scopus 로고
    • Structural genomics of proteins from conserved biochemical pathways and processes
    • Burley S.K., Bonanno J.B. Structural genomics of proteins from conserved biochemical pathways and processes. Curr. Opin. Struct. Biol. 12:2002;383-391.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 383-391
    • Burley, S.K.1    Bonanno, J.B.2
  • 22
    • 18244366113 scopus 로고    scopus 로고
    • An NMR approach to structural proteomics
    • This paper presents an NMR approach to structural genomics. The authors found 20% of the 500 small proteins that they have tested are amenable to NMR structure determination. They found that proteins from the thermophilic bacterium T. maritima had more well-behaved proteins on the basis of the expression, solubility and heteronuclear single quantum coherence (HSQC) results. By contrast, thermophilic properties of M. thermoautotrophicum proteins do not provide a significant advantage for structural genomics of small proteins using NMR. For a portion of 12 structures reported in the paper, putative functions have been inferred.
    • Yee A., Chang X., Pineda-Lucena A., Wu B., Semesi A., Le B., Ramelot T., Lee G.M., Bhattacharyya S., Gutierrez P.et al. An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. U.S.A. 99:2002;1825-1830 This paper presents an NMR approach to structural genomics. The authors found 20% of the 500 small proteins that they have tested are amenable to NMR structure determination. They found that proteins from the thermophilic bacterium T. maritima had more well-behaved proteins on the basis of the expression, solubility and heteronuclear single quantum coherence (HSQC) results. By contrast, thermophilic properties of M. thermoautotrophicum proteins do not provide a significant advantage for structural genomics of small proteins using NMR. For a portion of 12 structures reported in the paper, putative functions have been inferred.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 1825-1830
    • Yee, A.1    Chang, X.2    Pineda-Lucena, A.3    Wu, B.4    Semesi, A.5    Le, B.6    Ramelot, T.7    Lee, G.M.8    Bhattacharyya, S.9    Gutierrez, P.10
  • 24
    • 0012763164 scopus 로고    scopus 로고
    • Crystal structure and functional analysis of a hypothetical protein, MJ0882, from Methanococcus jannaschii
    • in press
    • Huang L, Hung LW, Kim R, Kim, SH: Crystal structure and functional analysis of a hypothetical protein, MJ0882, from Methanococcus jannaschii. J Struct Funct Genomics 2003, in press.
    • (2003) J Struct Funct Genomics
    • Huang, L.1    Hung, L.W.2    Kim, R.3    Kim, S.H.4
  • 25
    • 0035576364 scopus 로고    scopus 로고
    • Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine
    • Lim K., Zhang H., Tempczyk A., Bonander N., Toedt J., Howard A., Eisenstein E., Herzberg O. Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine. Proteins. 45:2001;397-407.
    • (2001) Proteins , vol.45 , pp. 397-407
    • Lim, K.1    Zhang, H.2    Tempczyk, A.3    Bonander, N.4    Toedt, J.5    Howard, A.6    Eisenstein, E.7    Herzberg, O.8
  • 26
    • 0036848698 scopus 로고    scopus 로고
    • The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase Is a methyltransferase
    • This paper describes an interesting example of structure-based reclassification of the enzymatic function of a protein. M. thermoautotrophicum MT0146/CbiT protein was originally annotated as precorrin-8w decarboxylase. The structure of MT0146 revealed an AdoMet-dependent methyltransferase fold and a bound AdoHcy. The authors suggest that all functional annotations in sequence and structure databases should cite the papers containing the primary experimental data establishing the functional assignment.
    • Keller J.P., Smith P.M., Benach J., Christendat D., deTitta G.T., Hunt J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase Is a methyltransferase. Structure. 10:2002;1475-1487 This paper describes an interesting example of structure-based reclassification of the enzymatic function of a protein. M. thermoautotrophicum MT0146/CbiT protein was originally annotated as precorrin-8w decarboxylase. The structure of MT0146 revealed an AdoMet-dependent methyltransferase fold and a bound AdoHcy. The authors suggest that all functional annotations in sequence and structure databases should cite the papers containing the primary experimental data establishing the functional assignment.
    • (2002) Structure , vol.10 , pp. 1475-1487
    • Keller, J.P.1    Smith, P.M.2    Benach, J.3    Christendat, D.4    DeTitta, G.T.5    Hunt, J.F.6
  • 27
    • 0034141555 scopus 로고    scopus 로고
    • Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution
    • Wang H., Boisvert D., Kim K.K., Kim R., Kim S.H. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution. EMBO J. 19:2000;317-323.
    • (2000) EMBO J. , vol.19 , pp. 317-323
    • Wang, H.1    Boisvert, D.2    Kim, K.K.3    Kim, R.4    Kim, S.H.5
  • 28
    • 0027536869 scopus 로고
    • Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly
    • Tollervey D., Lehtonen H., Jansen R., Kern H., Hurt E.C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell. 72:1993;443-457.
    • (1993) Cell , vol.72 , pp. 443-457
    • Tollervey, D.1    Lehtonen, H.2    Jansen, R.3    Kern, H.4    Hurt, E.C.5
  • 29
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics. 14:1998;755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 30
    • 0037025191 scopus 로고    scopus 로고
    • An alternative flavin-dependent mechanism for thymidylate synthesis
    • This paper describes the biochemical assay that establishes the flavin-dependent mechanism for the alternative thymidylate synthesis pathway.
    • Myllykallio H., Lipowski G., Leduc D., Filee J., Forterre P., Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 297:2002;105-107 This paper describes the biochemical assay that establishes the flavin-dependent mechanism for the alternative thymidylate synthesis pathway.
    • (2002) Science , vol.297 , pp. 105-107
    • Myllykallio, H.1    Lipowski, G.2    Leduc, D.3    Filee, J.4    Forterre, P.5    Liebl, U.6
  • 31
    • 0028871926 scopus 로고
    • DALI: A network tool for protein structure comparison
    • Holm L., Sander C. DALI: a network tool for protein structure comparison. Trends Biochem. Sci. 20:1995;478-480.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 32
    • 0030068703 scopus 로고    scopus 로고
    • HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae
    • Noskov V.N.et al. HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Yeast. 12:1996;17-29.
    • (1996) Yeast , vol.12 , pp. 17-29
    • Noskov, V.N.1
  • 33
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 34
    • 0036408348 scopus 로고    scopus 로고
    • Bonanno JB: Structuring the universe of proteins
    • Burley S.K. Bonanno JB: Structuring the universe of proteins. Annu. Rev. Genomics. Hum. Genet. 3:2002;243-262.
    • (2002) Annu. Rev. Genomics. Hum. Genet. , vol.3 , pp. 243-262
    • Burley, S.K.1
  • 35
    • 0036643498 scopus 로고    scopus 로고
    • Targeting novel folds for structural genomics
    • McGuffin L.J., Jones D.T. Targeting novel folds for structural genomics. Proteins. 48:2002;44-52.
    • (2002) Proteins , vol.48 , pp. 44-52
    • McGuffin, L.J.1    Jones, D.T.2
  • 36
    • 0033768266 scopus 로고    scopus 로고
    • Target selection for structural genomics
    • Brenner S.E. Target selection for structural genomics. Nat. Struct. Biol. 7:2000;967-969.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 967-969
    • Brenner, S.E.1
  • 37
    • 0036228236 scopus 로고    scopus 로고
    • Knowledge-based selection of targets for structural genomics
    • Frishman D. Knowledge-based selection of targets for structural genomics. Protein Eng. 15:2002;169-183.
    • (2002) Protein Eng. , vol.15 , pp. 169-183
    • Frishman, D.1
  • 38
    • 0036322695 scopus 로고    scopus 로고
    • Target space for structural genomics revisited
    • Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933.
    • (2002) Bioinformatics , vol.18 , pp. 922-933
    • Liu, J.1    Rost, B.2
  • 40
    • 0036330266 scopus 로고    scopus 로고
    • Selecting targets for structural determination by navigating in a graph of protein families
    • Portugaly E., Kifer I., Linial M. Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics. 18:2002;899-907.
    • (2002) Bioinformatics , vol.18 , pp. 899-907
    • Portugaly, E.1    Kifer, I.2    Linial, M.3
  • 42
    • 0035109680 scopus 로고    scopus 로고
    • Functional and structural genomics using PEDANT
    • Frishman D., Albermann K., Hani J., Heumann K., Metanomski A., Zollner A., Mewes H.W. Functional and structural genomics using PEDANT. Bioinformatics. 17:2001;44-57 This paper describes the software design of PEDANT, one of the most comprehensive structure annotation servers available ( http://pedant.gsf.de/ ).
    • (2001) Bioinformatics , vol.17 , pp. 44-57
    • Frishman, D.1    Albermann, K.2    Hani, J.3    Heumann, K.4    Metanomski, A.5    Zollner, A.6    Mewes, H.W.7
  • 43
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 44
    • 0036468055 scopus 로고    scopus 로고
    • Structural proteomics: Developments in structure-to-function predictions
    • Norin M., Sundstrom M. Structural proteomics: developments in structure-to-function predictions. Trends Biotechnol. 20:2002;79-84.
    • (2002) Trends Biotechnol. , vol.20 , pp. 79-84
    • Norin, M.1    Sundstrom, M.2


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