The ten-stranded β/α barrel in ribonucleotide reductase protein R1

Journal of Molecular Biology

Volumn 262, Issue 3, 1996, Pages 358-369

  Uhlin, Ulla ^a   Eklund, Hans ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Crystal structure; Ribonucleotide reductase; Structure comparison; TIM barrels; barrel

Indexed keywords

RIBONUCLEOTIDE REDUCTASE; TRIOSEPHOSPHATE ISOMERASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENERGY TRANSFER; HYDROGEN BOND; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENERGY TRANSFER; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RIBONUCLEOTIDE REDUCTASES; TRIOSE-PHOSPHATE ISOMERASE;

EID: 0030603925     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0519     Document Type: Article

References (56)

1. Åberg, A., Hahne, S., Karlsson, M., Larsson, A., Ormö, M., Åhgren, A. & Sjöberg, B.-M. (1989). Evidence for two classes of Redox-active cysteines in ribonucleotide reductase of Escherichia coli. J. Biol. Chem. 264, 12249-12252.
2. Andersson, I., Knight, S., Schneider, G., Lindqvist, Y., Lundqvist, T., Brändén, C.-I. & Lorimer, G. H. (1989). Crystal structure of the active site of ribulose 1,5-bisphosphate carboxylase. Nature, 337, 229-234.
3. Banner, D. W., Bloomer, A. C., Petsko, G. A., Phillips, D. C., Pogson, C. I., Wilson, I. A., Corran, P. H., Furth, A. J., Milman, J. D., Offord, R. E., Priddle, J. D. & Waley, S. G. (1975). Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data. Nature, 255, 609-614.
4. Brändén, C.-I. (1986). Anatomy of α/β proteins. In Computer Graphics and Molecular Modelling. Current Communications in Molecular Biology (Fletterick, R. & Zoller, M., eds), pp. 45-50, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
5. Brändén, C.-I. (1991). The TIM barrel - the most frequently occurring folding motif in proteins. Curr. Opinion. Struct. Biol. 1, 978-983.
6. Branden, C. & Tooze, J. (1991). Introduction to Protein Structure. Garland, New York.
7. Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
8. Climent, I., Sjöberg, B.-M. & Huang, C. Y. (1992). Site-directed mutagenesis and deletion of the carboxyl terminus of Escherichia coli ribonucleotide reductase protein R2. Biochemistry, 31, 4801-4807.
9. CCP4 (1994). Collaborative computational project, number 4: programs for protein crystallography. Acta Crystallog. sect. D, 50, 760-763.
10. Cowan, S. W. (1993). Bacterial porins: lessons from three high resolution structures. Curr. Opin. Struct. Biol. 3, 501-507.
11. Derewenda, U., Swenson, L., Green, R., Wei, Y., Dodson, G. G., Yamaguchi, S., Haas, M. J. & Derewenda, Z. S. (1994). An unusual buried polar cluster in a family of fungal lipases. Nature Struct. Biol. 1, 36-47.
12. Ekberg, M., Sahlin, M., Eriksson, M. & Sjöberg, B.-M. (1996). Two conserved residues in protein R1 participate in an intermolecular electron transfer in ribonucleotide reductase. J. Biol. Chem. In the press.
13. Engh, R. A. & Huber, R. (1992). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A, 47, 392-400.
14. Farber, G. K. & Petsko, G. A. (1990). The evolution of α/β barrel enzymes. Trends Biochem. Sci. 15, 228-234.
15. Farber, G. K., Glasfeld, A., Tiraby, G., Ringe, D. & Petsko, G. A. (1989). Crystallographic studies of the mechanism of xylose isomerase. Biochemistry, 28, 7289-7297.
16. Goldman, A., Ollis, D. I. & Steitz, T. A. (1987). Crystal structure of muconate lactonizing enzyme at 3 Å resolution. J. Mol. Biol. 194, 143-153.
17. Holmgren, A. (1980). Pyridine nucleotide - disulfide oxidoreductases. In Dehydrogenases Requiring Nicotinamide Coenzymes (Jeffery, J., ed.), pp. 149-180, Birkhäuser, Basel.
18. 2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263, 17857-17871.
19. Ito, N., Phillips, S. E. V., Stevens, C., Ogel, Z. B., Mcpherson, M. J., Keen, J. N., Yadav, K. D. S. & Knowles, P. F. (1991). Novel thioether bond revealed by a 1.7-Å crystal structure of galactose oxidase. Nature, 350, 87-90.
20. Jones, T. A., Cowan, S., Newcomer, M. E. & Bergfors, T. (1989). Crystallographic studies of two families of retinol binding protein. In Proc. Alfred Benzon Symp. 28, Munksgaard, Copenhagen, Denmark.
21. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. 47, 110-119.
22. Kleyweigt, G. J. (1994) Halloween ... Masks and Bones. In From First Map to Final Model, pp. 59-66, (Bailey, S., Hubbard, R. & Waller D. A., eds) SERC Daresbury Laboratory, Daresbury, UK.
23. Kraulis, P. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
24. Lebioda, L., Stec, B. & Brewer, J. M. (1989). The structure of yeast enolase at 2.25 Å resolution. J. Biol. Chem. 264, 3685-3693.
25. Lesk, A. M., Brändén, C.-I. & Chothia, C. (1989). Structural principles of α/β barrel proteins: the packing of the interior of the sheet. Proteins: Struct. Funct. Genet. 5, 139-148.
26. Licht, S., Gerfen, G. J. & Stubbe, J. (1996). Thiyl radicals in ribonucleotide reductases. Science, 271, 477-481.
27. Lindqvist, Y. (1989). Refined structure of spinach glycolate oxidase at 2 Å resolution. J. Mol. Biol. 209, 151-166.
28. 12 radicals are generated: the crystal structure of methylmalonylcoenzyme A mutase at 2 Å resolution. Structure, 4, 339-350.
29. Mao, S. S., Holler, T. P., Yu, G. X., Bollinger, J.-M., Booker, S., Johnston, M. I. & Stubbe, J. (1992). A model for the role of multiple cysteine residues involved in ribonucleotide reduction: amazing and still confusing. Biochemistry, 31, 9733-9743.
30. Moore, S. A. & James, M. N. G. (1995). Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.6 Å resolution. J. Mol. Biol. 249, 195-214.
31. Muirhead, H., Clayden, D. A., Barford, D., Lorimer, G., Fothergill-Gilmore, I. A., Schlitz, E. & Smitt, W. (1986). The structure of cat muscle pyruvate kinase. EMBO J. 5, 475-481.
32. Murshudov, G., Vagin, A. & Dodson, E. (1996). In The Refinement of Protein Structures. Proceedings of Daresbury Study Weekend. EU Validation contract: BIO2CT-92-0524.
33. Murzin, A. G., Lesk, A. M. & Chothia, C. (1994a). Principles determining the structure of β-sheet barrels in proteins. A theoretical analysis. J. Mol. Biol. 236, 1369-1381.
34. Murzin, A. G., Lesk, A. M. & Chothia, C. (1994b). Principles determining the structure of β-sheet barrels in proteins. The observed structures. J. Mol. Biol. 236, 1382-1400.
35. Neidhart, D. J., Kenyon, G. I., Gerlt, J. A. & Petsko, G. A. (1990). Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous. Nature, 347, 692-694.
36. Nikas, I., McLauchlan, J., Davison, A. J., Taylor, W. R. & Clements, B. (1986). Strutural features of ribonucleotide reductase. Proteins: Struct. Funct. Genet. 1, 376-384.
37. Nordlund, P., Sjöberg, B.-M. & Eklund, H. (1990). Three-dimensional structure of the free radical protein of ribonucleotide reductase. Nature, 345, 593-598.
38. Ollis, D. L., Chea, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. R., Silman, I., Schrag, J. L., Sussman, J. L., Verschueren, K. H. G. & Goldman, A. (1992). The α/β hydrolase fold. Protein Eng. 5, 197-211.
39. Otwinowski, Z. (1993). Data collection and processing. In Proceedings of the CCP4 Study Weekend (Sawyer, L., Issacs, N. & Bailey, S., eds), pp. 56-62, SERC Daresbury Laboratory, UK.
40. Pai, E. F. (1991). Variations on a theme: the family of FAD-dependent NAD(P)H-(disulphide)-oxidoreductases. Curr. Opin. Struct. Biol. 1, 796-803.
41. Reardon, D. & Farber, G. K. (1995). The structure and evolution of α/β barrel proteins. FASEB J. 9, 497-503.
42. Reichard, P. & Ehrenberg, A. (1983). Ribonucleotide reductase - a radical enzyme. Science, 221, 514-519.
43. Rondeau, J.-M., Tete-Favier, F., Podjarny, A., Reymann, J.-M., Barth, B., Biellmann, J.-F. & Moras, D. (1992). Novel NADPH-binding domain revealed by the crystal strcture of aldose reductase. Nature, 335, 469-472.
44. Rouvinen, J., Bergfors, T., Teeri, T., Knowles, J. K. C. & Jones, T. A. (1990). Three-dimensional structure of cellobiohydrolase 2 from Trichoderma reesei. Science, 249, 380-386.
45. Rova, U., Goodtzova, K., Ingemarson, R., Behravan, G., Gräslund, A. & Thelander, L. (1995). Evidence by site-directed mutagenesis supports long-range electron transfer in mouse ribonucleotide reductase. Biochemistry, 34, 4267-4275.
46. Scheerlinck, J.-P. Y., Lasters, I., Claessens, M., DeMaeyer, M., Pio, F., Delhaise, P. & Wodak, S. J. (1992). Recurrent αβ loop structure in TIM barrel motifs show a distinct pattern of conserved structural features. Proteins: Struct. Funct. Genet. 12, 299-313.
47. Schirmer, T., Keller, T. A., Wang, Y.-F. & Rosebusch, J. P. (1995). Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution. Science, 267, 512-514.
48. Stubbe, J. (1990). Ribonucleotide reductases. Advan. Enzymol. 63, 349-419.
49. Stubbe, J. & van der Donk, W. A. (1995). Ribonucleotide reductases: radical enzymes with suicidal tendencies. Chem. Biol. 2, 793-801.
50. Thelander, L. & Reichard, P. (1979). Reduction of ribonucleotides. Annu. Rev. Biochem. 48, 133-158.
51. Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallog. sect. A, 43, 489-501.
52. Uhlin, U. & Eklund, H. (1994). Structure of ribonucleotide reductase protein R1. Nature, 370, 533-539.
53. Uhlin, U., Uhlin, T. & Eklund, H. (1993). Crystallization and crystallographic investigations of the ribonucleotide reductase protein R1 of from Escherichia coli. FEBS Letters, 336, 148-152.
54. Weiss, M. S. & Schulz, G. E. (1992). Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227, 493-509.
55. Wilmanns, M., Hyde, C. C., Davies, D. R., Kirschner, K. & Jansonius, J. N. (1991). Stuctural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry, 30, 9161-9169.
56. 2 at 2.4 Å resolution. J. Mol. Biol. 212, 837-863.