Structural bases for sulfide recognition in Lucina pectinata hemoglobin I

Journal of Molecular Biology

Volumn 258, Issue 1, 1996, Pages 1-5

  Rizzi, Menico ^a   Wittenberg, Jonathan B ^b   Coda, Alessandro ^a   Ascenzi, Paolo ^c   Bolognesi, Martino ^a,d  

^a UNIVERSITY OF PAVIA   (Italy)

^b ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^c ROMA TRE UNIVERSITY   (Italy)

^d UNIVERSITY OF GENOA   (Italy)

Author keywords

Crystal structure; Heme protein; Monomeric mollusc hemoglobin; Sulfide carrier

Indexed keywords

HEMOGLOBIN; HEMOPROTEIN; PHENYLALANINE DERIVATIVE; SULFIDE;

ANION TRANSPORT; ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; DISSOCIATION; DRUG STABILITY; HYDROGEN BOND; LIGAND BINDING; MOLLUSC; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE;

LUCINA PECTINATA; MOLLUSCA;

EID: 0029945653     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0228     Document Type: Editorial

References (28)

1. Arp, A. J. (1991). The role of heme compounds in sulfide tolerance in the echiurian worm Urechis caupo. In Structure and function of Invertebrate Oxygen Carriers (Vinagradov, S. N. & Kapp, O. H., eds), pp. 337-346, Springer-Verlag, New York.
2. Bashford, D., Chothia, C. & Lesk, A. M. (1987). Determinants of a protein fold unique features of the globin amino acid sequences. J. Mol. Biol. 196, 199-216.
3. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: a computer based archival file for macromolecule structures. J. Mol. Biol. 112, 535-542.
4. Bisig, D. A., Di Iorio, E. E., Diederichs, K., Winterhalter, K. H. & Piontek, K. (1995). Crystal structure of asian elephant (Elephans maximus) cyanomet myoglobin at 1.78 Å resolution: Phe29(B10) accounts for its unusual ligand binding properties. J. Biol. Chem. 34, 8715-8725.
5. Brancaccio, A., Cutruzzola, F., Travaglini Allocatelli, C., Brunori, M., Smerdon, S. J., Wilkinson, A. J., Dou, Y., Keenan, D., Ikeda-Saito, M., Brantley, R. E. Jr & Olson, J. S. (1994). Structural factors governing azide and cyanide binding to mammalian met myoglobins. J. Biol. Chem. 269, 13843-13853.
6. Burley, S. K. & Petsko, G. A. (1985). Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science, 229, 23-28.
7. Carver, T. E., Olson, J. S., Smerdon, S. J., Krzywda, S. & Wilkinson, A. (1991). Contributions of residue 45(CD3) and heme-6-propionate to the bimolecular and germinate recombination reactions of myoglobin. Biochemistry, 30, 4697-4705.
8. Casale, E., Lionetti, C., Coda, A., Merli, A., Ascenzi, P., Wittenberg, J. B. & Bolognesi, M. (1991). Crystallization and preliminary data for the ferric form of Lucina pectinata hemoglobin I. J. Mol. Biol. 222, 447-449.
9. Collaborative computational project number 4 (1994). The CCP4 suite: programs for problem crystallography Acta Crystallog. sect. D, 50, 760-767.
10. Conti, E., Moser, C., Rizzi, M., Mattevi, A., Lionetti, C., Coda, A., Ascenzi, P., Brunori, M. & Bolognesi, M. (1993). X-ray crystal structure of Aplysia limacina myoglobin in different liganded states. J. Mol. Biol. 233, 498-508.
11. Dougherty D. A. & Stauffer, D. A. (1990). Acethylcholine binding by a synthetic receptor: implications for biological recognition. Science, 250, 1558-1560.
12. Hockenhull-Johnson, J., Stern, M. S., Martin, P., Dass, C., Desiderio, D. M., Wittenberg, J. B., Vinogradov, S. N. & Walz, D. A. (1991). The amino acid sequence of hemoglobin II from the symbiont-harboring clam Lucina pectinata. J. Protein Chem. 10, 609-622.
13. Hockenhull-Johnson, J., Stern, M. S., Wittenberg, J. B., Vinogradov, S. N., Kapp, O. H. & Walz, D. A. (1993). The amino acid sequence of hemoglobin III from the symbiont-harboring clam, Lucina pectinata. J. Protein Chem. 12, 261-277.
14. Kraus, D. W. & Wittenberg, J. B. (1990). Hemoglobins of the Lucina pectinata/bacteria symbiosis: I. molecular properties, kinetics and equilibria of reactions with ligands. J. Biol. Chem. 265, 16043-16053.
15. Kraus, D. W., Wittenberg, J. B., Jing-Fen, L. & Peisach, J. (1990). Hemoglobins of the Lucina pectinata/bacteria symbiosis: II. an electron paramagnetic resonance and optical spectra study of the ferric proteins. J. Biol. Chem. 265, 16054-16059.
16. Navaza, J. (1994). AMoRe: an automatic package for molecular replacement. Acta Crystallog. sect. A, 50, 157-163.
17. Orpen, A. G. & Brammer, L. (1989). Tables of bond lengths determined by X-ray and neutron diffraction: part 2. organometallic compounds and co-ordination complexes of the d- and f-block metals. Chem. Soc. Dalton Trans. S1-S83.
18. Perutz, M. F. (1989). Myoglobin and haemoglobin: role of distal residues in reactions with haem ligands. Trends Biochem. Sci. 14, 42-44.
19. Perutz, M. F. (1990). Mechanisms regulating the reactions of human hemoglobin with oxygen and carbon monoxide. Annu. Rev. Physiol. 52, 1-25.
20. Reid, K. S. C., Lindley P. F. & Thornton, J. M. (1985). Sulphur-aromatic interactions in proteins. FEBS Letters, 190, 209-213.
21. Rizzi, M., Wittenberg, J. B., Coda, A., Fasano, M., Ascenzi, P & Bolognesi, M. (1994). Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata: crystallographic analysis at 1.5 A resolution. J. Mol. Biol. 244, 86-99.
22. Smerdon, S. J., Krzywda, S., Brzozowski, A. M., Davies, G. J., Wilkinson, A. J., Brancaccio, A., Cutruzzola', F., Travaglini Allocatelli, C., Brunori, M., Li, T., Brantley, R. E. Jr, Carver, T. E., Eich, R. F., Singleton, E. & Olson, J. S. (1995). Interactions among residues CD3, E7, E10 and E11 in myoglobins: attempts to simulate the ligand binding properties of Aplysia limacina. Biochemistry, 34, 8715-8725.
23. Springer, B. A., Sligar, S. G., Olson, J. S. & Phillips, G. N. Jr (1994). Mechanisms of ligand recognition in myoglobin. Chem. Rev. 94, 699-714.
24. Thomas, K. A., Smith, G. M., Thomas, T. B. & Feldmann, R. J. (1982). Electronic distributions within protein phenylalanine aromatic rings are reflected by the three dimensional oxygen atom environments. Proc. Natl Acad. Sci. USA, 79, 4843-4847.
25. 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.
26. Vinogradov, S. N., Walz, D. A., Pohajdak, B., Moens, L., Kapp, O. H., Suzuki, T. & Trotman, C. N. A. (1993). Adventitious variability? The amino acid sequences of nonvertebrate globins. Comp. Biochem. Physiol. 106B, 1-26.
27. Wittenberg, J. B. & Kraus, D. W. (1991). Hemoglobins of eukaryote/prokaryote symbioses. In Structure and Function of Invertebrate Oxygen Carriers (Vinagradov, S. N. & Kapp, O. H., eds), pp. 323-330, Springer-Verlag, New York.
28. Yang, J., Kloek, A. P., Goldberg, D. E. & Mathews, F. S. (1995). The structure of Ascaris hemoglobin domain I at 2.2 Å resolution: molecular features of oxygen avidity Proc. Natl Acad. Sci. USA, 92, 4224-4228.