Refinement of the three-dimensional structures of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.67 Å resolution and from Desulfovibrio desulfuricans ATCC 27774 at 1.6 Å resolution

Simões, Pedro; Matías, Pedro M.; Morais, J.; Wilson, K. S.; Dauter, Zbigniew; Carrondo, M.A.

doi:10.1016/s0020-1693(97)06018-0

Cited by 43 publications

(44 citation statements)

References 21 publications

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“…In the , plots for the non-proline and nonglycine residues (not shown) only Cys-51 in both molecules lies outside the normally allowed regions, as previously discussed (14). Overall, 88.0% of the non-proline and non-glycine residues for the reduced form (82.6% for the oxidized form) lie within the most favored regions.…”

Section: Methodssupporting

confidence: 60%

“…It must be noted that at pH 7.6 the structures are expected to represent the fully deprotonated oxidized state (pK a ox ϭ 4.6 and 5.0), and a partially protonated condition in the reduced state (pK a red ϭ 7.6 and 7.1). Thus, to assess the changes linked only to reduction, the structure models of both redox states were also compared with the structure of the oxidized state at pH 4.0 previously reported (14). The models of both redox states at pH 7.6 were superimposed with X-PLOR (28) using the main-chain and heme ring atoms.…”

Section: Resultsmentioning

confidence: 99%

“…Structure Determination and Refinement-The positioning of the previously obtained structural model for the oxidized form of Ddc3 at room temperature and pH 4.0 (14) in the crystal structures of the oxidized and reduced forms at 110 K and pH 7.6 was carried out by the molecular replacement method with the program AmoRe (15) using data up to 3.5-Å resolution. Clear solutions were obtained for both forms, with correlation coefficients of 69.8 and 68.8%, and R-factors of 33.0 and 34.2%, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome

Louro¹,

Bento²,

Matías³

et al. 2001

Journal of Biological Chemistry

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Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c 3 is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechanochemical coupling involved in the transfer of multiple electrons and protons in cytochrome c 3 from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.Recent developments in techniques of structural biology have opened the way for probing the mechanisms used by biological macromolecules involved in energy transduction at the molecular level. The structural analysis of bacteriorhodopsin trapped in the M photointermediate state (1), the structures in the oxidized and reduced forms of cytochromes c 3 that perform a coupled two-electron step associated with proton transfer (2, 3), and the establishment of the coupled transfer of electrons and protons to the 3Fe-4S cluster of Azotobacter vinelandii ferredoxin (4) are just a few recent examples where results from different techniques are integrated in a description at the atomic level of the energy-transducing events. The phenomenon of energy transduction relies on coupled events (5), whether they involve only electrostatic interactions or structural rearrangements of the active sites or its surroundings (mechano-chemical coupling), which may be more important than the electrostatic component of the overall coupling (6). The pumping of proton(s) at the beginning of re-reduction of cytochrome c oxidase (7) can be described using a model in which the electrostatic attraction of electrons and protons is overcome (8), a situation that requires structural changes involving charged residues. Small proteins capable of performing energy transduction provide easier access to the structural bases for the underlying mechanisms, as the recent advances in the understanding of the proton pumping by the 26-kDa bacteriorhodopsin demonstrate (1, 9).This wo...

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Section: Methodssupporting

confidence: 60%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome

Louro¹,

Bento²,

Matías³

et al. 2001

Journal of Biological Chemistry

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“…Up to now the X-ray crystal structures of cytochromes c 3 from D. desulfuricans Norway (DdN), 23 D. vulgaris Miyazaki (DvM), 24 D. vulgaris Hildenborough (DvH), 25 and D. gigas (Dg) 26 were solved. A single-crystal EPR study carried out on DdN cytochrome c 3 permitted a direct assignment of the g z values to hemes H 1 -H 4 defined in the crystal structure.…”

Section: G Values Of Low-spin Hemes In Cytochromes Cmentioning

confidence: 99%

EPR spectroscopy: A powerful technique for the structural and functional investigation of metalloproteins

Moré¹,

Belle²,

Asso³

et al. 1999

Biospectroscopy

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“…Using coordinates retrieved from the Protein Data Bank (44), a more detailed comparison is included below between the different domains of HmcA, and the TpI-c 3 and TpII-c 3 folds, as well as the integral 9HcA fold, represented by the 9HcA from Dd27k (PDB 19HC) (16). The TpI-c 3 structure chosen as a model for comparisons was that of DvH (PDB 2CTH) (52), and the TpII-c 3 structure is that of Da (PDB 3CAO) (49). A comparison of the three-heme domain with the triheme cytochrome c 3 (cyt.c 7 ) from Dac (PDB 1HH5) (53) is also included.…”

Section: Resultsmentioning

confidence: 99%

Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

Matías

Coelho

Valente

et al. 2002

Journal of Biological Chemistry

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The crystal structure of the high molecular mass cytochrome c HmcA from Desulfovibrio vulgaris Hildenborough is described. HmcA contains the unprecedented number of sixteen hemes c attached to a single polypeptide chain, is associated with a membranebound redox complex, and is involved in electron transfer from the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. The structure of HmcA is organized into four tetraheme cytochrome c 3 -like domains, of which the first is incomplete and contains only three hemes, and the final two show great similarity to the nine-heme cytochrome c from Desulfovibrio desulfuricans. An isoleucine residue fills the vacant coordination space above the iron atom in the five-coordinated high-spin Heme 15. The characteristics of each of the tetraheme domains of HmcA, as well as its surface charge distribution, indicate this cytochrome has several similarities with the nine-heme cytochrome c and the Type II cytochrome c 3 molecules, in agreement with their similar genetic organization and mode of reactivity and further support an analogous physiological function for the three cytochromes. Based on the present structure, the possible electron transfer sites between HmcA and its redox partners (namely Type I cytochrome c 3 and other proteins of the Hmc complex), as well as its physiological role, are discussed.

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Refinement of the three-dimensional structures of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.67 Å resolution and from Desulfovibrio desulfuricans ATCC 27774 at 1.6 Å resolution

Cited by 43 publications

References 21 publications

Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome

Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome

EPR spectroscopy: A powerful technique for the structural and functional investigation of metalloproteins

Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

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