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. 1999 Dec;8(12):2655–2662. doi: 10.1110/ps.8.12.2655

The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex.

S J Lloyd 1, H Lauble 1, G S Prasad 1, C D Stout 1
PMCID: PMC2144235  PMID: 10631981

Abstract

The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.

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Selected References

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  1. Beinert H., Kiley P. Redox control of gene expression involving iron-sulfur proteins. Change of oxidation-state or assembly/disassembly of Fe-S clusters? FEBS Lett. 1996 Mar 11;382(1-2):218–221. doi: 10.1016/0014-5793(96)00140-8. [DOI] [PubMed] [Google Scholar]
  2. Beinert Helmut, Kennedy Mary Claire, Stout C. David. Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein. Chem Rev. 1996 Nov 7;96(7):2335–2374. doi: 10.1021/cr950040z. [DOI] [PubMed] [Google Scholar]
  3. Emptage M. H., Dreyers J. L., Kennedy M. C., Beinert H. Optical and EPR characterization of different species of active and inactive aconitase. J Biol Chem. 1983 Sep 25;258(18):11106–11111. [PubMed] [Google Scholar]
  4. Flint D. H., Emptage M. H., Finnegan M. G., Fu W., Johnson M. K. The role and properties of the iron-sulfur cluster in Escherichia coli dihydroxy-acid dehydratase. J Biol Chem. 1993 Jul 15;268(20):14732–14742. [PubMed] [Google Scholar]
  5. Flint Dennis H., Allen Ronda M. Ironminus signSulfur Proteins with Nonredox Functions. Chem Rev. 1996 Nov 7;96(7):2315–2334. doi: 10.1021/cr950041r. [DOI] [PubMed] [Google Scholar]
  6. Green J., Bennett B., Jordan P., Ralph E. T., Thomson A. J., Guest J. R. Reconstitution of the [4Fe-4S] cluster in FNR and demonstration of the aerobic-anaerobic transcription switch in vitro. Biochem J. 1996 Jun 15;316(Pt 3):887–892. doi: 10.1042/bj3160887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Haile D. J., Rouault T. A., Harford J. B., Kennedy M. C., Blondin G. A., Beinert H., Klausner R. D. Cellular regulation of the iron-responsive element binding protein: disassembly of the cubane iron-sulfur cluster results in high-affinity RNA binding. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):11735–11739. doi: 10.1073/pnas.89.24.11735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kennedy M. C., Beinert H. The state of cluster SH and S2- of aconitase during cluster interconversions and removal. A convenient preparation of apoenzyme. J Biol Chem. 1988 Jun 15;263(17):8194–8198. [PubMed] [Google Scholar]
  9. Kent T. A., Emptage M. H., Merkle H., Kennedy M. C., Beinert H., Münck E. Mössbauer studies of aconitase. Substrate and inhibitor binding, reaction intermediates, and hyperfine interactions of reduced 3Fe and 4Fe clusters. J Biol Chem. 1985 Jun 10;260(11):6871–6881. [PubMed] [Google Scholar]
  10. Khoroshilova N., Popescu C., Münck E., Beinert H., Kiley P. J. Iron-sulfur cluster disassembly in the FNR protein of Escherichia coli by O2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological activity. Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6087–6092. doi: 10.1073/pnas.94.12.6087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lauble H., Kennedy M. C., Beinert H., Stout C. D. Crystal structures of aconitase with isocitrate and nitroisocitrate bound. Biochemistry. 1992 Mar 17;31(10):2735–2748. doi: 10.1021/bi00125a014. [DOI] [PubMed] [Google Scholar]
  12. Lauble H., Kennedy M. C., Beinert H., Stout C. D. Crystal structures of aconitase with trans-aconitate and nitrocitrate bound. J Mol Biol. 1994 Apr 8;237(4):437–451. doi: 10.1006/jmbi.1994.1246. [DOI] [PubMed] [Google Scholar]
  13. Lazazzera B. A., Beinert H., Khoroshilova N., Kennedy M. C., Kiley P. J. DNA binding and dimerization of the Fe-S-containing FNR protein from Escherichia coli are regulated by oxygen. J Biol Chem. 1996 Feb 2;271(5):2762–2768. doi: 10.1074/jbc.271.5.2762. [DOI] [PubMed] [Google Scholar]
  14. McRee D. E. XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. J Struct Biol. 1999 Apr-May;125(2-3):156–165. doi: 10.1006/jsbi.1999.4094. [DOI] [PubMed] [Google Scholar]
  15. Merritt E. A., Murphy M. E. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. doi: 10.1107/S0907444994006396. [DOI] [PubMed] [Google Scholar]
  16. Robbins A. H., Stout C. D. Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal. Proc Natl Acad Sci U S A. 1989 May;86(10):3639–3643. doi: 10.1073/pnas.86.10.3639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rouault T. A., Klausner R. D. Iron-sulfur clusters as biosensors of oxidants and iron. Trends Biochem Sci. 1996 May;21(5):174–177. [PubMed] [Google Scholar]
  18. Rouault T. A., Stout C. D., Kaptain S., Harford J. B., Klausner R. D. Structural relationship between an iron-regulated RNA-binding protein (IRE-BP) and aconitase: functional implications. Cell. 1991 Mar 8;64(5):881–883. doi: 10.1016/0092-8674(91)90312-m. [DOI] [PubMed] [Google Scholar]
  19. Schloss J. V., Emptage M. H., Cleland W. W. pH profiles and isotope effects for aconitases from Saccharomycopsis lipolytica, beef heart, and beef liver. alpha-Methyl-cis-aconitate and threo-Ds-alpha-methylisocitrate as substrates. Biochemistry. 1984 Sep 25;23(20):4572–4580. doi: 10.1021/bi00315a010. [DOI] [PubMed] [Google Scholar]
  20. Skala J., Capieaux E., Balzi E., Chen W. N., Goffeau A. Complete sequence of the Saccharomyces cerevisiae LEU1 gene encoding isopropylmalate isomerase. Yeast. 1991 Apr;7(3):281–285. doi: 10.1002/yea.320070310. [DOI] [PubMed] [Google Scholar]
  21. Zheng L., Andrews P. C., Hermodson M. A., Dixon J. E., Zalkin H. Cloning and structural characterization of porcine heart aconitase. J Biol Chem. 1990 Feb 15;265(5):2814–2821. [PubMed] [Google Scholar]
  22. Zheng L., Kennedy M. C., Beinert H., Zalkin H. Mutational analysis of active site residues in pig heart aconitase. J Biol Chem. 1992 Apr 15;267(11):7895–7903. [PubMed] [Google Scholar]

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