Structural and mutational studies of the carboxylate cluster in iron-free ribonucleotide reductase R2

Biochemistry

Volumn 43, Issue 24, 2004, Pages 7966-7972

  Andersson, Martin E ^a   Högbom, Martin ^a,c   Rinaldo Matthis, Agnes ^a   Blodig, Wolfgang ^a   Liang, Yuhe ^b   Persson, Bert Ove ^a   Sjöberg, Britt Marie ^a   Su, Xiao Dong ^b   Nordlund, Pär ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b PEKING UNIVERSITY   (China)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLATION; ESCHERICHIA COLI; HYDRATION; HYDROGEN BONDS; MOLECULAR STRUCTURE; MUTAGENESIS; PROTEINS;

PROTONATION STATES; STRUCTURAL VARIATIONS;

BIOCHEMISTRY;

APOPROTEIN; BACTERIAL PROTEIN; CARBOXYLIC ACID; HISTIDINE; IRON; MUTANT PROTEIN; RIBONUCLEOTIDE REDUCTASE; RIBONUCLEOTIDE REDUCTASE R2; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CORYNEBACTERIUM; CORYNEBACTERIUM AMMONIAGENES; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDRATION; HYDROGEN BOND; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT; SITE DIRECTED MUTAGENESIS; WILD TYPE; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; CARBOXYLIC ACIDS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA PRIMERS; IRON; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; RIBONUCLEOTIDE REDUCTASES;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); CORYNEBACTERIUM; CORYNEBACTERIUM AMMONIAGENES; ESCHERICHIA COLI; NEGIBACTERIA; UNCULTURED ACTINOMYCETE;

EID: 2942729758     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi036088l     Document Type: Article

References (25)

1. Nordlund, P., Sjöberg, B.-M., and Eklund, H. (1990) Three-dimensional structure of the free radical protein of ribonucleotide reductase, Nature 345, 593-598.
2. Lippard, S. J., and Berg, J. M. (1994) Principles of Bioinorganic Chemistry, University Science Books, Sausalito, CA.
3. Williams, R. J. P., and Silvia, J. J. R. F. d. (1996) The Natural Selection of the Chemical Elements: The Environment and Life's Chemistry, Clarendon Press, Oxford, U.K.
4. Fersht, A. (1985) Enzyme Structure and Mechanism, W. H. Freeman and Company, New York.
5. Iwata, S., Ostermeier, C., Ludwig, B., and Michel, H. (1995) Structure at 2.8 Å Resolution of Cytochrome c Oxidase from Paracoccus denitrificans, Nature 376, 660-669.
6. Heberle, J. (2000) Proton-transfer reactions across bacteriorhodopsin and along the membrane, Biochim. Biophys. Acta Bioenerg. 1458, 135-147.
7. Åberg, A., Nordlund, P., and Eklund, H. (1993) Unusual clustering of carboxyl side-chains in the core of iron-free ribonucleotide reductase, Nature 361, 276-278.
8. Logan, D. T., Su, X. D., Åberg, A., Regnström, K., Hajdu, J., Eklund, H., and Nordlund, P. (1996) Crystal structure of reduced protein R2 of ribonucleotide reductase: The structural basis for oxygen activation at a dinuclear iron site, Structure 4, 1053-1064.
9. Keech, A. M., Le Brun, N. E., Wilson, M. T., Andrews, S. C., Moore, G. R., and Thomson, A. J. (1997) Spectroscopic studies of cobalt(II) binding to Escherichia coli bacterioferritin, J. Biol. Chem. 272, 422-429.
10. Michel, H. (1999) Cytochrome c oxidase: Catalytic cycle and mechanisms of proton pumping - A discussion, Biochemistry 38, 15129-15140.
11. Hoganson, C. W., and Babcock, G. T. (1997) A metalloradical mechanism for the generation of oxygen from water in photosynthesis, Science 277, 1953-1956.
12. 3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: Evidence for new reaction cycle intermediates, Biochemistry 37, 2131-2144.
13. Andersson, M. E., Högbom, M., Rinaldo-Matthis, A., Andersson, K. K., Sjöberg, B. M., and Nordlund, P. (1999) The crystal structure of an azide complex of the diferrous R2 subunit of ribonucleotide reductase displays a novel carboxylate shift with important mechanistic implications for diiron-catalyzed oxygen activation, J. Am. Chem. Soc. 121, 2346-2352.
14. Persson, B. O., Karlsson, M., Climent, I., Ling, J. S., Loehr, J. S., Sahlin, M., and Sjöberg, B. M. (1996) Iron ligand mutants in protein R2 of Escherichia coli ribonucleotide reductase-Retention of diiron site, tyrosyl radical, and enzymatic activity in mutant proteins lacking an iron-binding side chain, J. Biol. Inorg. Chem. 1, 247-256.
15. Sjöberg, B.-M., Hahne, S., Karlsson, M., Jörnvall, H., Göransson, M., and Uhlin, B. E. (1986) Overproduction and purification of the B2 subunit of ribonucleotide reductase from Escherichia coli, J. Biol. Chem. 261, 5658-5662.
16. Nordlund, P., Uhlin, U., Westergren, C., Joelsen, T., Sjöberg, B. M., and Eklund, H. (1989) New crystal forms of the small subunit of ribonucleotide reductase from Escherichia coli, FEBS Lett. 258, 251-254.
17. Högbom, M., Huque, Y., Sjöberg, B. M., and Nordlund, P. (2002) Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes, Biochemistry 41, 1381-1389.
18. Kabsch, W. (1988) J. Appl. Crystallogr. 21, 916-924.
19. Otwinowski, Z. (1993) pp 56-62, SERC Daresbury Laboratory, Warrington, U.K.
20. Collaborative computational project (1994) Acta Crystallogr., Sect. C 50, 760-763.
21. Brünger A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination, Acta Crystallogr., Sect. D 54, 905-921.
22. Logan, D. T., deMaré, F., Persson, B. O., Slaby, A., Sjöberg, B. M., and Nordlund, P. (1998) Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: Structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins, Biochemistry 37, 10798-10807.
23. Creighton, T. (1993) Proteins, W. H. Freeman and Company, New York.
24. Perrin, C. L., and Nielson, J. B. (1997) "Strong" hydrogen bonds in chemistry and biology, Annu. Rev. Phys. Chem. 48, 511-544.
25. Rammelsberg, R., Huhn, G., Lubben, M., and Gerwert, K. (1998) Bacteriorhodopsin's intramolecular proton-release pathway consists of a hydrogen-bonded network, Biochemistry 37, 5001-5009.