Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity

EMBO Reports

Volumn 9, Issue 2, 2008, Pages 157-163

  Nardini, Marco ^a   Pesce, Alessandra ^b   Thijs, Liesbet ^c   Saito, Jennifer A ^d   Dewilde, Sylvia ^c   Alam, Maqsudul ^d   Ascenzi, Paolo ^e   Coletta, Massimiliano ^f   Ciaccio, Chiara ^f   Moens, Luc ^c   Bolognesi, Martino ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

^c UNIVERSITY OF ANTWERP   (Belgium)

^d UNIVERSITY OF HAWAII   (United States)

^e ROMA TRE UNIVERSITY   (Italy)

^f UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARBON DIOXIDE; CYTOGLOBIN; GLOBIN; HEMOGLOBIN; HEMOPROTEIN; MATRIX PROTEIN; NEUROGLOBIN; NITRIC OXIDE; OXYGEN; PROTOGLOBIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; METHANOSARCINA; METHANOSARCINA ACETIVORANS; MOLECULAR CLONING; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE;

ARCHAEAL PROTEINS; CARBON MONOXIDE; CRYSTALLOGRAPHY, X-RAY; DIFFUSION; HEME; KINETICS; LIGANDS; METHANOSARCINA; MODELS, MOLECULAR; OXYGEN; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

ARCHAEA; METHANOSARCINA ACETIVORANS;

EID: 38949170616     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/sj.embor.7401153     Document Type: Article

References (37)

1. Antonini E, Brunori M (1971) Hemoglobin and Myoglobin in their Reactions with Ligands. Amsterdam, London: North Holland Publishing Co
2. Bateman H (1910) Solution of a system of differential equations occurring in the theory of radio-active transformations. Proc Cambridge Phyl Soc 15: 423-427
3. Berman HM, Westbrook J, Fenz Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28: 235-242
4. Bolognesi M, Cannillo E, Ascenzi P, Giacometti GM, Merli A, Brunori M (1982) Reactivity of ferric Aplysia and sperm whale myoglobins towards imidazole. X-ray and binding study. J Mol Biol 158: 305-315
5. Bolognesi M, Bordo D, Rizzi M, Tarricone C, Ascenzi P (1997) Nonvertebrate hemoglobins: Structural bases for reactivity. Prog Biophys Mol Biol 68: 29-68
6. Bolognesi M, Boffi A, Coletta M, Mozzarelli A, Pesce A, Tarricone C, Ascenzi P (1999) Anticooperative ligand binding properties of recombinant ferric Vitreoscilla homodimeric hemoglobin: A thermodynamic, kinetic and X-ray crystallographic study. J Mol Biol 291: 637-650
7. Brunori M, Gibson QH (2001) Cavities packing defects in the structural dynamics of myoglobin. EMBO Rep 2: 674-679
8. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760-763
9. Dewilde S, Kiger L, Burmester T, Hankeln T, Baudin-Creuza V, Aerts T, Marden MC, Caubergs R, Moens L (2001) Biochemical characterization and ligand binding properties of neuroglobin, a novel member of the globin family. J Biol Chem 276: 38949-38955
10. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132
11. Evans PR (1993) Proceedings of the CCP4 Study Weekend, on Data Collection and Processing, pp 114-122. Warrington, UK: CLRC Daresbury Laboratory
12. Farrés J, Rechsteiner MP, Herold S, Frey AD, Kallio PT (2005) Ligand binding properties of bacterial hemoglobins and flavohemoglobins. Biochemistry 44: 4125-4134
13. Ferry JG, House CH (2006) The stepwise evolution of early life driven by energy conservation. Mol Biol Evol 23: 1286-1296
14. Freitas TAK, Hou S, Dioum EM, Saito J, Newhouse J, Gonzalez G, Gilles-Gonzalez M-A, Alam M (2004) Ancestral hemoglobins in Archaea. Proc Natl Acad Sci USA 101: 6675-6680
15. Galagan JE et al (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12 532-542
16. Giangiacomo L, Mattu M, Arcovito A, Bellenchi G, Bolognesi M, Ascenzi P, Boffi A (2001) Monomer-dimer equilibrium and oxygen binding properties of ferrous Vitreoscilla hemoglobin. Biochemistry 40: 9311-9316
17. Giangiacomo L, Hari A, Boffi A, Morea V, Chiancone E. (2005) The truncated oxygen-avid hemoglobin from Bacillus subtilis X-ray structure and ligand binding properties. J Biol Chem 280: 9192-9202
18. Gibson QH (1973) The contribution of the α and β chains fb the kinetics of oxygen binding to and dissociation from hemoglobin. Proc Natl Acad Sci USA 70: 1-4
19. Hou S et al (2001) Globin-coupled sensors: A class of heme-containing sensors in Archaea and Bacteria. Proc Natl Acad Sci USA 98: 9353-9358
20. Krissinel E, Henrick K (2003) Detection of protein assemblies in crystals. In CompLife 2005, Berthold-MR et al (eds) LNBI 3695, pp 163-174. Berlin Heidelberg, Germany: Springer
21. Laskowski RA (1995) SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J Mol Graph 13: 323-330
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK, a program to-check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283-291
23. Leslie AGM (2003) MOSFLM User Guide, Mosflm Version 6.2.3. Cambridge UK: MRC Laboratory of Molecular Biology
24. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proc Natl Acad Sci USA 103: 17921-17926
25. Milani M et al (2005) Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins. J Inorg Biochem 99: 97-109
26. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240-255
27. Perrakis A, Morris R, Lamzin V (1999) Automated protein model building, combined with iterative structure refinement. Nat Struct Biol 6 458-463
28. Rother M, Metcalf WW (2004) Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide: An unusual way of life for a methanogenic archaeon. Proc Natl Acad Sci USA 101: 16929-16934
29. Shelnutt JA, Song X-Z, Ma J-G, Jia S-L, Jentzen W, Medforth CJ (1998) Nonpolar porphyrins and their significance in proteins. Chem Soc Rev 27: 31-41
30. Smerdon SJ et al (1995) Interactions among residues CD3, E7, E10, and E11 in myoglobins: Attempts to simulate the ligand-binding properties of Aplysia myoglobin. Biochemistry 34: 8715-8725
31. Storoni LC, McCoy AJ, Read RJ (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr D Biol Crystallogr 60: 432-438
32. Terwilliger TC, Berendzen J (1999) Automated structure solution for MIR and MAD. Acta Crystallogr D Biol Crystallogr 55: 849-861
33. Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren J (2006) A phylogenomic profile of globins. BMC Evol Biol 6: 31
34. Vinogradov SN, Hoogewijs D, Bailly X, Mizuguchi K, Dewilde S, Moens L, Vanfleteren J (2007) A model of globin evolution. Gene 398: 132-142
35. Wright E, Serpersu EH (2004) Isolation of aminoglycoside nucleotidyltransferase (2")-la from inclusion bodies as active, monomeric enzyme. Protein Expr Purif 35: 373-380
36. Zhang W, Phillips Jr GN (2003) Structure of the oxygen sensor in Bacillus subtilis: Signal transduction of chemotaxis by control of symmetry. Structure 11: 1097-1110
37. Zhang W, Olson JS, Phillips Jr GN (2005) Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis. Biophys J 88: 2801-2814