PerspectiveStructural Biology

Complex II Is Complex Too

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Science  31 Jan 2003:
Vol. 299, Issue 5607, pp. 671-672
DOI: 10.1126/science.1081821

In aerobic eukaryotic cells, the generation of energy in the form of adenosine triphosphate (ATP) [HN1] is mainly driven by the activity of the respiratory chain enzymes of the mitochondrial inner membrane [HN2]. The respiratory chain [HN3]—composed of enzyme complexes I to IV, ubiquinone [HN4], cytochrome c [HN5], and ATP synthase (complex V)—transfers electrons from NADH and succinate [HN6] at one end to molecular oxygen at the other (1). On page 700 of this issue, Yankovskaya et al. [HN7] (2) present the x-ray crystal structure at 2.6 Å resolution of the bacterial version of eukaryotic complex II. This enzyme, called succinate:quinone oxidoreductase (SQR) [HN8] in Escherichia coli, couples the two-electron oxidation of succinate forming fumarate [HN9], to the reduction of ubiquinone (3). SQR, which is also the succinate dehydrogenase of the Krebs cycle [HN10], is crucial for intermediary metabolism and energy production in eukaryotic cells and bacteria under aerobic conditions.

Eukaryotic complex II and E. coli SQR are composed of four protein subunits and five prosthetic groups [HN11]. The two largest subunits bind to one flavin adenine dinucleotide (FAD) [HN12] and three iron-sulfur cluster prosthetic groups. These two hydrophilic protein subunits are linked to a pair of hydrophobic protein subunits, which form a membrane anchor that binds to one heme group and provides ubiquinone with a binding site. The SQR structure reveals that electrons are transferred in a path more than 40 Å in length from the succinate oxidation site at the FAD, by way of the three iron-sulfur clusters, to the ubiquinone binding site (see the figure). One iron-sulfur cluster, the heme group, and bound ubiquinone are positioned at the corners of a triangle. The edge-to-edge distance between individual pairs of these redox components is 11 Å or less, a distance appropriate for rapid electron transfer. The heme in the E. coli SQR can be reduced by succinate, but based on the structure, this does not seem to be obligatory for the transfer of electrons from succinate to ubiquinone.

The intricacies of complex II.

Eukaryotic complex II (equivalent to SQR in E. coli) directly connects the respiratory chain of the inner mitochondrial membrane with the Krebs cycle enzymes in the mitochondrial matrix. Complex I (NADH:quinone oxidoreductase) and complex II reduce ubiquinone (Q) to ubiquinol (QH2). Complex III (quinone:cytochrome c reductase) uses ubiquinol to reduce cytochrome c, which is reoxidized by reduction of molecular oxygen to water catalyzed by complex IV (cytochrome c oxidase). Complexes I, III, and IV couple electron transfer to the formation of a transmembrane proton gradient that drives ATP synthesis by complex V (not shown). The x-ray crystal structure of E. coli SQR (2) with its four protein subunits (purple, orange, green, and blue ribbons) is shown in the position of complex II. Visible in the crystal structure is FAD (gold), oxaloacetate (green), three iron-sulfur clusters (red, iron; yellow, sulfur), ubiquinone (light blue), heme b (magenta), and cardiolipin (pale yellow). (The respiratory chain complexes are not drawn to scale.)

CREDIT: CRYSTAL STRUCTURE IMAGE, R. HORSEFIELD AND S. IWATA

Yankovskaya and colleagues present the crystal structure of E. coli SQR in a complex with either ubiquinone or an inhibitor that blocks binding of ubiquinone. The two structures elegantly pinpoint where on SQR the reduction of ubiquinone takes place. Other revelations include the presence of two tightly bound, well-ordered phospholipids; the architecture of the ubiquinone-binding pocket; and the spatial arrangement of heme and ubiquinone. It is reassuring to find that the crystal structure of E. coli SQR is consistent with most of the predictions based on other types of experimental data (4).

Dehydrogenases that oxidize an organic substrate and reduce ubiquinone often consist of only one polypeptide and a flavin moiety as the prosthetic group. Examples of such simple membrane-associated enzymes in E. coli include NADH dehydrogenase type II, D-lactate dehydrogenase, and aerobic glycerol-3-phosphate dehydrogenase (5). The enzymatic tasks of these dehydrogenases and of succinate dehydrogenase (SQR) seem similar, so it is all the more surprising that SQR has five different prosthetic groups. Perhaps SQR carries out additional, as yet unrecognized, tasks such as sensing the amount of molecular oxygen (6). Saraste [HN13] emphasized the intricate nature of SQR, compared with respiratory complexes I, III and IV, in his phrase “complex II is complex too.” Despite its intricacies, SQR is not directly involved in energy transduction (the coupling of electron transfer to the formation of a transmembrane proton gradient that drives ATP synthesis).

The composition of E. coli SQR is also puzzling when compared with that of its close relative fumarate reductase (QFR). Detailed comparison is now possible as crystal structures are available for the QFRs of E. coli and another bacterium, Wolinella succinogenes (7, 8). [HN14] The extracellular domains of SQR and the two QFRs are very similar in composition and overall structure, but the membrane-anchor domains differ in their structure and particularly in the number of heme groups that they bind. E. coli QFR contains no heme but has binding sites for two menaquinone molecules, QP and QD; the W. succinogenes QFR contains two heme groups, bP and bD. The position of the single heme group in the E. coli SQR roughly corresponds to that of QP and heme bP in the QFRs. Intriguingly, a cavity in SQR filled with two acyl chains of a cardiolipin phospholipid molecule corresponds to the location of QD and heme bD in the QFRs. Thus, the three available structures reveal considerable diversity in redox components within a protein scaffold of common evolutionary origin. Although the SQR and QFR of E. coli can functionally replace each other, SQR operates under aerobic conditions and QFR under anaerobic conditions. The SQR crystal structure of Yankovskaya et al. reveals a possible explanation for why SQR is the favored enzyme when oxygen is present.

Under aerobic conditions, reduced E. coli QFR is autooxidized at the FAD, producing large amounts of reactive oxygen species, including superoxide anion radical (·O2) and hydrogen peroxide (H2O2) (9). [HN15] The production is first order with respect to oxygen concentration, and the rate-limiting step is the formation of ·O2. The extent of reduction of the enzyme influences whether the released product is mainly ·O2 or H2O2. In sharp contrast, E. coli SQR reacts poorly with molecular oxygen, producing modest amounts of ·O2 and no H2O2. Differences in accessibility of the flavin moiety to molecular oxygen, the redox properties of FAD, and the properties of neighboring redox groups and cooperative electromagnetic interactions between these groups affect the reactivity of the flavin moiety. On the basis of their crystal structure and other data, Yankovskaya et al. argue that the heme group in SQR is pivotal in preventing the formation of reactive oxygen species at FAD. They also point out that mutations identified in human complex II—for example, those causing tumors in patients with hereditary paraganglioma—could lead to increased production of reactive oxygen species by SQR, resulting either directly or indirectly in tissue damage and disease. [HN16]

Crystal structures are now available for seven of the eight enzymes of the Krebs cycle and for the entire succinate oxidase system, that is, complexes II, III, and IV, and cytochrome c. But obtaining the structures of complex I and parts of complex V remain formidable challenges. Although complex II has yet to reveal all of its secrets, the Yankovskaya et al. crystal structure of E. coli SQR brings us a giant step closer to a full appreciation of the intricacies of this enzyme.

HyperNotes Related Resources on the World Wide Web

General Hypernotes

Dictionaries and Glossaries

The xrefer Web site provides a searchable collection of scientific dictionaries and other references.

The On-line Medical Dictionary is provided by CancerWeb.

D. Glick's Glossary of Biochemistry and Molecular Biology is made available by Portland Press.

A glossary of protein structure is available from the VHG (Virtual HyperGlossary) Web site.

The IUPAC Compendium of Chemical Terminology is available (with definitions in PDF format) from the International Union of Pure and Applied Chemistry.

IUPAC's glossary of terms used in bioinorganic chemistry and a nomenclature of electron-transfer proteins are among the resources available on the chemical nomenclature and biochemical nomenclature Web sites provided by G. P. Moss, Department of Chemistry, Queen Mary University of London.

Web Collections, References, and Resource Lists

P. Gannon's Cell & Molecular Biology Online is a collection of annotated links to Internet resources.

BUBL LINK, maintained by the Strathclyde University Library, UK, offers links to Internet resources on biochemistry and molecular biology and crystallography.

The Google Web Directory provides links to Internet resources on biochemistry.

Crystallography Online is provided by the International Union of Crystallography.

CrystaLinks - A Crystallographer's Miscellany is maintained by E. Merritt, Biomolecular Structure Center, University of Washington.

The Protein Data Bank (PDB) is a repository for the processing and distribution of 3-D biological macromolecular structure data. A presentation on the nature of 3-D structural data and a collection of links to educational resources are provided.

Membrane Proteins of Known Structure is a compilation with links maintained by the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.

The World Index of BioMolecular Visualization Resources is provided by E. Martz, University of Massachusetts.

Molecular Models for Biochemistry is presented by W. McClure, Department of Biological Sciences, Carnegie Mellon University.

A Chime Molecular Image Gallery is provided by G. Gray, Department of Chemistry and Physics, Southwest Baptist University, Bolivar, MO.

Online Texts and Lecture Notes

The companion Web site for the third edition of Biochemistry by C. Mathews, K. van Holde, and K. Ahern provides introductions to concepts, molecules, and enzymes.

The Molecules of Life is a presentation by the Laboratory of Molecular Biophysics, University of Oxford, UK, about the techniques used to study protein structure. An introduction to X-ray crystallography is included.

A tutorial on X-ray crystallography is provided by M. Weiss, European Molecular Biology Laboratory, Hamburg.

Crystallography 101 is a Web tutorial by B Rupp, X-ray Crystallography and Structural Genomics Group, Lawrence Livermore National Laboratory.

The Structural Medicine Division, Department of Haematology, University of Cambridge, UK, makes available lecture notes for a course on protein crystallography.

An Internet tutorial on biochemistry and biophysics of redox proteins is provided by Ö. Hansson, Department of Biochemistry and Biophysics, Göteborg University, Sweden.

G. Rule, Department of Biological Sciences, Carnegie Mellon University, offers lecture notes for a biochemistry course.

R. Paselk, Department of Chemistry, Humboldt State University, Arcata, CA, provides lecture notes for a biochemistry course. Lecture notes on mitochondrial electron transport (parts one and two) are included.

J. Diwan, Department of Biology, Rensselaer Polytechnic Institute, offers lecture notes for a course on the biochemistry of metabolism. Presentations on the Krebs cycle and the electron transfer chain are included.

A. Crofts, Department of Biochemistry, University of Illinois, offers lecture notes for a course on biological energy conversion.

J. Illingworth, Department of Biochemistry and Molecular Biology, University of Leeds, UK, provides a collection of lecture presentations on bioenergetics.

General Reports and Articles

The 5 March 1999 issue of Science had a review article by M. Saraste titled “Oxidative phosphorylation at the fin de siècle.”

The 17 January 2002 issue of Biochimica et Biophysica Acta (BBA) - Bioenergetics was a special issue on succinate:ubiquinone oxidoreductase. The contents of this sample issue are available online and include an introductory article by C. R. D. Lancaster titled “Succinate:quinone oxidoreductases — An overview.”

From the NCBI Bookshelf: Molecular Biology of the Cell by B. Alberts et al. includes a chapter on energy conversion in mitochondria and chloroplasts, and Molecular Cell Biology by H. Lodish et al. has a section on electron transport and oxidative phosphorylation in the chapter on cellular energetics.

Numbered Hypernotes

1. Adenosine triphosphate. ATP (adenosine triphosphate) is defined in xrefer's Dictionary of Science. The Biochemistry companion Web site offers an introduction to ATP. The online Columbia Encyclopedia provides an introduction to ATP. ATP was featured as a molecule of the month. M. Farabee's On-Line Biology Book includes a section on ATP and biological energy. Kimball's Biology Pages include an introduction to ATP.

2. Mitochondria. Cells Alive! provides an introduction to mitochondria. M. Farabee's On-Line Biology Book offers an introduction to mitochondria. The Cell Biology Web Pages, provided by G. Childs, University of Arkansas for Medical Sciences, include a presentation on mitochondrial structure and function. The 5 March 1999 issue of Science had a review article by M. Yaffe titled “The machinery of mitochondrial inheritance and behavior.”

3. Respiratory (electron transport) chain of mitochondria. Electron transport chain is defined in xrefer's Dictionary of Science. The Biochemistry companion Web site provides an introduction to the electron transport system. The Microbe Library makes available an animation of electron transport in mitochondria. Kimball's Biology Pages offer a presentation on cellular respiration. The microbiology Web site of G. Kaiser, Division of Mathematics, Science and Engineering, Community College of Baltimore County, Catonsville, provides an introduction to the electron transport chain. The Neuromuscular Disease Center, Washington University, offers a presentation on the mitochondrial respiratory chain. J. Illingworth offers a presentation on respiratory chain components. K. Redding, Department of Chemistry, University of Alabama, Tuscaloosa, offers lecture notes on the respiratory electron transport chain for a biochemistry course. P. von Sengbusch's Botany Online includes a presentation on the respiratory chain.

4. Ubiquinone (coenzyme Q) is defined in xrefer's Dictionary of Biology. The Biochemistry companion Web site offers an introduction to coenzyme Q (ubiquinone).

5. Cytochrome c. The Biochemistry companion Web site provides an introduction to cytochromes. Cytochrome c and cytochrome c oxidase were featured as a PDB molecule of the month. The Institute of Molecular BioSciences, Massey University, New Zealand, makes available a tutorial on cytochrome c.

6. NADH and succinate are defined in xrefer's Dictionary of Biology. Introductions to NADH and succinate are provided by the Biochemistry companion Web site. P. von Sengbusch's Botany Online includes a section on NADH in the presentation on hydrogen acceptors.

7. V. Yankovskaya and G. Cecchini are in the Molecular Biology Division, VA Medical Center, San Francisco. R. Horsefield, B. Byrne, and S. Iwata are in the Department of Biological Sciences, Imperial College London. S. Törnroth is in the Department of Biochemistry, Uppsala University, Sweden. C. Luna-Chavez is at the Center for Biophysics and Computational Biology, University of Illinois. H. Miyoshi is in the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan. C. Léger is at BIP07-CNRS, Marseille, France.

8. Succinate:quinone oxidoreductase (SQR) (succinate dehydrogenase). The Biochemistry companion Web site offers an introduction to succinate dehydrogenase. A. Crofts makes available a presentation on succinate:quinone oxidoreductase (SQR). G. Rule offers a presentation on succinate dehydrogenase in the lecture notes on electron transport for a biochemistry course. The Armstrong Research Group, Department of Chemistry, University of Oxford, provides a research presentation on succinate dehydrogenase. C. R. D. Lancaster, Max Planck Institute of Biophysics, makes available (in PDF format) a handbook chapter on SQR.

9. Fumarate is defined by the Biochemistry companion Web site.

10. Krebs cycle (citric acid cycle). Krebs cycle (citric acid cycle; tricarboxylic acid cycle; TCA cycle) is defined in xrefer's Dictionary of Science. Citric acid cycle is defined in the glossary of Lodish et al.'s Molecular Cell Biology, which also provides a graphic representation of the citric acid cycle. The online Columbia Encyclopedia has an introduction to the Krebs cycle. G. Kaiser offers an introduction to the Krebs cycle. A citric acid cycle tutorial is provided by G. Gray. L. Buehler, Biology Department, University of California, San Diego, offers lecture notes on the citric acid cycle for a course on metabolic biochemistry. R. Paselk provides lecture notes on the Krebs cycle (parts one and two) for a biochemistry course. W. McClure's Molecular Models for Biochemistry includes a presentation on the TCA cycle.

11. Subunit and prosthetic group are defined in the glossary of terms used in bioinorganic chemistry. The glossary of protein structure defines subunit. Prosthetic group is defined (in PDF format) in the IUPAC Compendium of Chemical Terminology.

12. Flavin adenine dinucleotide. FAD (flavin adenine dinucleotide) is defined in xrefer's Dictionary of Biology. The Biochemistry companion Web site offers an introduction to introduction to FAD. P. von Sengbusch's Botany Online includes a section on FAD in the presentation on hydrogen acceptors.

13. A memorial page for Matti Saraste is provided by the European Molecular Biology Laboratory.

14. Fumarate reductase (QFR) crystal structures of Escherichia coli and Wolinella succinogenes. A. Crofts offers tutorials on fumarate reductase of E. coli and fumarate reductase of W. succinogenes. The 25 November 1999 issue of Nature had an article by C. R. D. Lancaster, A. Kröger, M. Auer, and H. Michel titled “Structure of fumarate reductase from Wolinella succinogenes at 2.2 _ resolution.” The Max Planck Society for the Advancement of Science issued a news release about this research. The 18 June 1999 issue of Science had an report by T. Iverson, C. Luna-Chavez, G. Cecchini, and D. Rees titled “Structure of the Escherichia coli fumarate reductase respiratory complex” and a Perspective by L. Hederstedt titled “Respiration without O2.” The Berkeley Lab's Advanced Light Source offers a presentation titled “Structure of a key link in the respiratory chain” about the E. coli fumarate reductase research. The Armstrong Research Group offers a research presentation on E. coli fumarate reductase.

15. Reactive oxygen species. An introduction to reactive oxygen is provided by the Biochemistry companion Web site. Kimball's Biology Pages offer a presentation on reactive oxygen species. R&D Systems makes available a mini-review on reactive oxygen species. G. Buettner and L. Oberley, Free Radical and Radiation Biology Program, University of Iowa College of Medicine, make available a collection of student papers (in PDF format) for a course on free radicals in biology and medicine; papers on hydrogen peroxide and superoxide are included. The 27 August 2002 issue of the Journal of Biological Chemistry had an article by K. Messner and J. Imlay titled “Mechanism of superoxide and hydrogen peroxide formation by fumarate reductase, succinate dehydrogenase, and aspartate oxidase.”

16. Complex II-related disorders such as hereditary paraganglioma. Online Mendelian Inheritance in Man has an entry for hereditary paraganglioma. The Neuromuscular Disease Center provides information on paragangliomas. The May 2002 issue of the European Journal of Genetics had an article by P. Rustin, A. Munnich, and A. Rötig titled “Succinate dehydrogenase and human diseases: New insights into a well-known enzyme.” The December 2001 issue of the American Journal of Human Genetics had an article by A.-P. Gimenez-Roqueplo et al. titled “The R22X mutation of the SDHD gene in hereditary paraganglioma abolishes the enzymatic activity of complex II in the mitochondrial respiratory chain and activates the hypoxia pathway.” The 4 February 2002 issue of Science had a report by B. Baysal et al. titled “Mutations in SDHD, a mitochondrial complex II gene, in hereditary paraganglioma.” The 5 March 1999 issue had a review article by D. Wallace titled “Mitochondrial diseases in man and mouse.”

17. L. Hederstedt is in the Department of Cell and Organism Biology, Lund University, Sweden.

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