Abstract
The aerobic respiratory chain of the thermohalophilic bacterium Rhodothermus marinus, a nonphotosynthetic organism from the Bacteroidetes/Chlorobi group, contains a high-potential iron–sulfur protein (HiPIP) that transfers electrons from a bc 1 analog complex to a caa 3 oxygen reductase. Here, we describe the crystal structure of the reduced form of R. marinus HiPIP, solved by the single-wavelength anomalous diffraction method, based on the anomalous scattering of the iron atoms from the [4Fe–4S]3+/2+ cluster and refined to 1.0 Å resolution. This is the first structure of a HiPIP isolated from a nonphotosynthetic bacterium involved in an aerobic respiratory chain. The structure shows a similar environment around the cluster as the other HiPIPs from phototrophic bacteria, but reveals several features distinct from those of the other HiPIPs of phototrophic bacteria, such as a different fold of the N-terminal region of the polypeptide due to a disulfide bridge and a ten-residue-long insertion.
Similar content being viewed by others
Abbreviations
- HiPIP:
-
High-potential iron–sulfur protein
- RmHip:
-
Rhodothermus marinus high-potential iron–sulfur protein
- SLS:
-
Swiss Light Source
- Tris:
-
Tris(hydroxymethyl)aminomethane
- Rms:
-
Root mean square
References
Huber C, Wachtershauser G (1998) Science 281:670–672
Beinert H (2000) J Biol Inorg Chem 5:2–15
Yagi T, Matsuno-Yagi A (2003) Biochemistry 42:2266–2274
Kennel SJ, Bartsch RG, Kamen MD (1972) Biophys J 12:882–896
Pereira MM, Antunes AM, Nunes OC, da Costa MS, Teixeira M (1994) FEBS Lett 352:327–330
Pereira MM, Carita JN, Teixeira M (1999) Biochemistry 38:1276–1283
Hochkoeppler A, Kofod P, Zannoni D (1995) FEBS Lett 375:197–200
Klinge S, Hirst J, Maman JD, Krude T, Pellegrini L (2007) Nat Struct Mol Biol 14:875–877
Weiner BE, Huang H, Dattilo BM, Nilges MJ, Fanning E, Chazin WJ (2007) J Biol Chem 282:33444–33451
Hamann N, Mander GJ, Shokes JE, Scott RA, Bennati M, Hedderich R (2007) Biochemistry 46:12875–12885
Pereira PM, Teixeira M, Xavier AV, Louro RO, Pereira IA (2006) Biochemistry 45:10359–10367
Lukianova OA, David SS (2005) Curr Opin Chem Biol 9:145–151. doi:10.1016/j.cbpa.2005.02.006
Meyer TE, Przysiecki CT, Watkins JA, Bhattacharyya A, Simondsen RP, Cusanovich MA, Tollin G (1983) Proc Natl Acad Sci USA 80:6740–6744
Van Driessche G, Vandenberghe I, Devreese B, Samyn B, Meyer TE, Leigh R, Cusanovich MA, Bartsch RG, Fischer U, Van Beeumen JJ (2003) J Mol Evol 57:181–199
Santana M, Pereira MM, Elias NP, Soares CM, Teixeira M (2001) J Bacteriol 183:687–699
Ausubel FM, Brent R, Kingstone RE, Moore DD, Seidman JG, Smith JA, Struhl K (1995) Current protocols in molecular biology. Greene Publishing Associates/Wiley Interscience, New York
da Costa PN, Teixeira M, Saraiva LM (2003) FEMS Microbiol Lett 218:385–393
Leslie AGW (1992) Joint CCP4+ESF-EAMCB Newslett Protein Crystallogr 26
Collaborative Computational Project N (1994) Acta Crystallogr D Biol Crystallogr 50:760–763
Uson I, Sheldrick GM (1999) Curr Opin Struct Biol 9:643–648
Sheldrick GM (2003) SHELXC. University of Göttingen, Göttingen
Sheldrick GM (2002) Z Kristallogr 217:644–650
Morris RJ, Perrakis A, Lamzin VS (2002) Acta Crystallogr D Biol Crystallogr 58:968–975
Emsley P, Cowtan K (2004) Acta Crystallogr D Biol Crystallogr 60:2126–2132
Lamzin VS, Wilson KS (1997) Methods Enzymol 277:269–305
Sheldrick GM, Schneider TR (1997) Methods Enzymol 277:319–343
McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ (2005) Acta Crystallogr D Biol Crystallogr 61:458–464
Engh RA, Huber R (1991) Acta Crystallogr A 47:392–400
Kabsch W, Sander C (1983) Biopolymers 22:2577–2637
Krissinel E, Henrick K (2007) J Mol Biol 372:774–797
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Nucleic Acids Res 25:3389–3402
Sali A, Blundell TL (1993) J Mol Biol 234:779–815
DeLano WL (2002) PyMOL. DeLano Scientific, Palo Alto
Tullman-Ercek D, DeLisa MP, Kawarasaki Y, Iranpour P, Ribnicky B, Palmer T, Georgiou G (2007) J Biol Chem 282:8309–8316
Carter CW Jr, Kraut J, Freer ST, Xuong NH, Alden RA, Bartsch RG (1974) J Biol Chem 249:4212–4225
Liu L, Nogi T, Kobayashi M, Nozawa T, Miki K (2002) Acta Crystallogr D Biol Crystallogr 58:1085–1091
Kerfeld CA, Salmeen AE, Yeates TO (1998) Biochemistry 37:13911–13917
Benning MM, Meyer TE, Rayment I, Holden HM (1994) Biochemistry 33:2476–2483
Breiter DR, Meyer TE, Rayment I, Holden HM (1991) J Biol Chem 266:18660–18667
Gonzalez A, Benini S, Ciurli S (2003) Acta Crystallogr D Biol Crystallogr 59:1582–1588
Rayment I, Wesenberg G, Meyer TE, Cusanovich MA, Holden HM (1992) J Mol Biol 228:672–686
Nouailler M, Bruscella P, Lojou E, Lebrun R, Bonnefoy V, Guerlesquin F (2006) Extremophiles 10:191–198
Frazao C, Aragao D, Coelho R, Leal SS, Gomes CM, Teixeira M, Carrondo MA (2008) FEBS Lett 582:763–767
Beeby M, O’Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO (2005) PLoS Biol 3:e309
Backes G, Mino Y, Loehr TM, Meyer TE, Cusanovich MA, Sweeney WV, Adman ET, Sanders-Loehr J (1991) J Am Chem Soc 113:2055–2064
Adman E, Watenpaugh KD, Jensen LH (1975) Proc Natl Acad Sci USA 72:4854–4858
Jensen GM, Warshel A, Stephens PJ (1994) Biochemistry 33:10911–10924
Babini E, Borsari M, Capozzi F, Eltis LD, Luchinat C (1999) J Biol Inorg Chem 4:692–700
Soriano A, Li D, Bian S, Agarwal A, Cowan JA (1996) Biochemistry 35:12479–12486
Agarwal A, Li D, Cowan JA (1995) Proc Natl Acad Sci USA 92:9440–9444
Stelter M, Melo AM, Pereira MM, Gomes CM, Hreggvidsson GO, Hjorleifsdottir S, Saraiva LM, Teixeira M, Archer M (2008) Biochemistry 47:11953–11963
Srinivasan V, Rajendran C, Sousa FL, Melo AM, Saraiva LM, Pereira MM, Santana M, Teixeira M, Michel H (2005) J Mol Biol 345:1047–1057
Hochkoeppler A, Kofod P, Ferro G, Ciurli S (1995) Arch Biochem Biophys 322:313–318
Acknowledgments
We are grateful to Nuno A.M. Félix for excellent technical assistance, to Ana Coelho, from the Mass Spectrometry Service of Instituto de Tecnologia Química e Biológica, and to João Carita for cell growth. We thank Carlos Frazão for advice on high-resolution refinement and the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities. X-ray data collection at SLS was supported by the European Commission under the Sixth Framework Programme through the Key Action: Strengthening the European Research Area, Research Infrastructures, contract no. RII3-CT-2004-506008. This work was supported by Fundação para a Ciência e a Tecnologia (PTDC/BIA-PRO/66833/2006 to M.A., POCTI/BIA-PRO/58608/2004 to M.T., REEQ/336/BIO/05, PTDC/BIA-PRO/67105/2006 to A.M.P.M.). M.S. received a grant from Fundação para a Ciência e a Tecnologia (BPD/24193/2005).
Author information
Authors and Affiliations
Corresponding author
Additional information
M. Stelter and A. M. P. Melo contributed equally to this work.
The Rhodothermus marinus high-potential iron–sulfur protein coordinates and structure factors have been deposited in the Protein Data Bank with accession code 3H31.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Stelter, M., Melo, A.M.P., Hreggvidsson, G.O. et al. Structure at 1.0 Å resolution of a high-potential iron–sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus . J Biol Inorg Chem 15, 303–313 (2010). https://doi.org/10.1007/s00775-009-0603-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00775-009-0603-8