Structure of the Escherichia coli fumarate reductase respiratory complex

Science

Volumn 284, Issue 5422, 1999, Pages 1961-1966

  Iverson, Tina M ^a   Luna Chavez, César ^b,c   Cecchini, Gary ^b,c   Rees, Douglas C ^d  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b SAN FRANCISCO VETERANS AFFAIRS MEDICAL CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CITRIC ACID; FLAVINE ADENINE NUCLEOTIDE; FUMARATE REDUCTASE; PROTON PUMP; QUERCETIN; QUINONE DERIVATIVE; SUCCINATE DEHYDROGENASE; UBIQUINOL CYTOCHROME C REDUCTASE;

ANAEROBIC METABOLISM; ARTICLE; BACTERIAL METABOLISM; CELL ENERGY; CITRIC ACID CYCLE; COVALENT BOND; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; ENERGY TRANSFER; ENZYME ANALYSIS; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; RESPIRATORY CHAIN;

AEROBIOSIS; ANAEROBIOSIS; BINDING SITES; CELL MEMBRANE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTRON TRANSPORT; ENERGY METABOLISM; ESCHERICHIA COLI; FLAVIN-ADENINE DINUCLEOTIDE; FUMARATES; IRON-SULFUR PROTEINS; MODELS, MOLECULAR; OXIDATION-REDUCTION; OXYGEN CONSUMPTION; PROTEIN CONFORMATION; PROTEIN FOLDING; QUINONES; SUCCINATE DEHYDROGENASE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0033580880     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.284.5422.1961     Document Type: Article

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26. 1 with unit cell constants a = 96.6 Å, b = 138.1 Å, and c = 275.3 Å and two complexes per asymmetric unit. The oxidation state of the enzyme cannot be clearly established in this structure.
27. Data were collected by the inverse beam method at - 180°C at beam line 5.0.2 at the Advanced Light Source with an ADSC Quantum4 charge-coupled device. Wavelengths for optimal data collection were determined with a single-crystal EXAFS (extended x-ray absorption fine structure) scan. Data were processed with DENZO and scaled with SCALEPACK [Z. Otwinoski and W. Minor, Methods Enzymol. 276, 307 (1997)] and the CCP4 suite of programs (32).
28. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
29. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
30. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
31. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
32. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
33. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
34. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
35. cryst for 2% of the reflections omitted from the refinement totaling 1005 Bijvoet pairs. The rmsd of bond lengths and angles is 0.02 Å and 1.9°, respectively, with less than 1% of the residues having disallowed values for the Φ and Ψ angles according to a Ramachandran diagram. The final model for each complex contains 8467 atoms in residues 1 to 575 (of 601 total residues) of FrdA, 1 to 243 (of 243 total residues) of FrdB, 1 to 130 (of 130 total residues) of FrdC, and 1 to 118 (of 118 residues) of FrdD, as well as a [2Fe:2S] cluster, a [3Fe:4S] cluster, a [4Fe:4S] cluster, a FAD, an oxaloacetate molecule, two menaquinone molecules, and one molecule of ordered detergent. The initiator methionine has been excluded from residue numbering because it is believed to be cleaved from the mature protein (3), consistent with the lack of electron density seen before residue 1 of each protein in the complex.
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66. Crystal contacts in the membrane-spanning region of a protein are relatively unusual, but have previously been seen in the structure of the iron transporter FhuA [K. P. Locher, B. Rees, D. Moras, J. P. Rosenbusch, in G-Protein-Coupled Receptors T. Haga, Ed. (CRC Monographs, CRC Press, Boca Raton, FL, in press); K. P. Locher et al., Cell 95, 771 (1998)], porins (S. W. Cowen et al., Nature 358, 727 (1992)], and bacteriorhodopsin, which was crystallized in the presence of cubic lipids [E. Pebay-Peyroula, G. Rummel, J. P. Rosenbusch, E. M. Landau, Science 277, 1676 (1997)].
67. Crystal contacts in the membrane-spanning region of a protein are relatively unusual, but have previously been seen in the structure of the iron transporter FhuA [K. P. Locher, B. Rees, D. Moras, J. P. Rosenbusch, in G-Protein-Coupled Receptors T. Haga, Ed. (CRC Monographs, CRC Press, Boca Raton, FL, in press); K. P. Locher et al., Cell 95, 771 (1998)], porins (S. W. Cowen et al., Nature 358, 727 (1992)], and bacteriorhodopsin, which was crystallized in the presence of cubic lipids [E. Pebay-Peyroula, G. Rummel, J. P. Rosenbusch, E. M. Landau, Science 277, 1676 (1997)].
68. Crystal contacts in the membrane-spanning region of a protein are relatively unusual, but have previously been seen in the structure of the iron transporter FhuA [K. P. Locher, B. Rees, D. Moras, J. P. Rosenbusch, in G-Protein-Coupled Receptors T. Haga, Ed. (CRC Monographs, CRC Press, Boca Raton, FL, in press); K. P. Locher et al., Cell 95, 771 (1998)], porins (S. W. Cowen et al., Nature 358, 727 (1992)], and bacteriorhodopsin, which was crystallized in the presence of cubic lipids [E. Pebay-Peyroula, G. Rummel, J. P. Rosenbusch, E. M. Landau, Science 277, 1676 (1997)].
69. Crystal contacts in the membrane-spanning region of a protein are relatively unusual, but have previously been seen in the structure of the iron transporter FhuA [K. P. Locher, B. Rees, D. Moras, J. P. Rosenbusch, in G-Protein-Coupled Receptors T. Haga, Ed. (CRC Monographs, CRC Press, Boca Raton, FL, in press); K. P. Locher et al., Cell 95, 771 (1998)], porins (S. W. Cowen et al., Nature 358, 727 (1992)], and bacteriorhodopsin, which was crystallized in the presence of cubic lipids [E. Pebay-Peyroula, G. Rummel, J. P. Rosenbusch, E. M. Landau, Science 277, 1676 (1997)].
70. All figures were made with MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)) or BOBSCRIPT [R. Esnouf, J. Mol. Graph. 15, 133 (1997)] and rendered with RASTER3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994)].
71. All figures were made with MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)) or BOBSCRIPT [R. Esnouf, J. Mol. Graph. 15, 133 (1997)] and rendered with RASTER3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994)].
72. All figures were made with MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)) or BOBSCRIPT [R. Esnouf, J. Mol. Graph. 15, 133 (1997)] and rendered with RASTER3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994)].
73. Supported by the Department of Veterans Affairs, NIH, and NSF (G.C. and C.L-C.), and the Howard Hughes Medical Institute and NIH (D.C.R.). T.M.I. is supported by an NIH training grant. We thank I. Schröder, S. I. Chan, S. C. Hung, and the members of the Rees group for discussions; K. H. Tubman and T. D. Tubman for critical reading; and J. J. Ottesen and T. N. Earnest for experimental assistance. The Advanced Light Source is supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Materials Sciences Division, of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098 at Lawrence Berkeley National Laboratory.