[[Image:heme.gif |frame|left| Figure 2. The tetrapyrrolic heme prosthetic group that can either be covalently attached to or closely associated with various proteins, such as cytochromes and other globin proteins. In ''Rm''cyt''c'', R2 is an ethyl group covalently attached to Cys 45, and R3 is a methyl group covalently attached to Cys48.]]
[[Image:heme.gif |frame|left| Figure 2. The tetrapyrrolic heme prosthetic group that can either be covalently attached to or closely associated with various proteins, such as cytochromes and other globin proteins. In ''Rm''cyt''c'', R2 is an ethyl group covalently attached to Cys 45, and R3 is a methyl group covalently attached to Cys48.]]
{{Clear}}
The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wraps around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main /> One final note is the number of <scene name='Sandbox_Reserved_335/Met/1'>methionine</scene> residues that ''Rm''cyt''c'' contains. In general, cyt ''c'' contains about two methionines whereas ''Rm''cyt''c'' contains seven, located on the left of the heme.<ref name=main />
The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wraps around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main /> One final note is the number of <scene name='Sandbox_Reserved_335/Met/1'>methionine</scene> residues that ''Rm''cyt''c'' contains. In general, cyt ''c'' contains about two methionines whereas ''Rm''cyt''c'' contains seven, located on the left of the heme.<ref name=main />
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In the electron transport chain (ETC), cyt ''c'' shuttles electrons between the respiratory complexes III and IV; complex III is the cytochrome ''bc''<sub>1</sub> complex and IV is cyt ''c'' oxidase. Initially, the heme iron in cyt ''c'' is in the reduced, Fe<sup>3+</sup> state; this allows for the uptake of one electron, oxidizing the iron to the Fe<sup>2+</sup> state.<ref name='etc'>Karp, Gerald (2008). Cell and Molecular Biology (5th edition). Hoboken, NJ: John Wiley & Sons. ISBN 978-0470042175.</ref> The ETC in eukaryotes is quite simple compared to that of prokaryotes (Figure 3).
In the electron transport chain (ETC), cyt ''c'' shuttles electrons between the respiratory complexes III and IV; complex III is the cytochrome ''bc''<sub>1</sub> complex and IV is cyt ''c'' oxidase. Initially, the heme iron in cyt ''c'' is in the reduced, Fe<sup>3+</sup> state; this allows for the uptake of one electron, oxidizing the iron to the Fe<sup>2+</sup> state.<ref name='etc'>Karp, Gerald (2008). Cell and Molecular Biology (5th edition). Hoboken, NJ: John Wiley & Sons. ISBN 978-0470042175.</ref> The ETC in eukaryotes is quite simple compared to that of prokaryotes (Figure 3).
[[Image:Etc.gif |frame|left| |size|300| Figure 3. The electron transport chain of a) eukaryotes as compared to b) prokaryotes.]]
[[Image:Etc.gif |frame|left|thumb|400px| Figure 3. The electron transport chain of a) eukaryotes as compared to b) prokaryotes.]]
In prokaryotic systems, electrons can enter the ETC at a number of places and multiple donors can be in play; however, the underlying transport system remains the same. Electrons are ultimately transferred from donor to various redox complexes including the ''bc''<sub>1</sub> complex and cytochrome ''c'', and finally to a terminal electron acceptor such as molecular oxygen in eukaryotes.<ref name=etc />
In prokaryotic systems, electrons can enter the ETC at a number of places and multiple donors can be in play; however, the underlying transport system remains the same. Electrons are ultimately transferred from donor to various redox complexes including the ''bc''<sub>1</sub> complex and cytochrome ''c'', and finally to a terminal electron acceptor such as molecular oxygen in eukaryotes.<ref name=etc />
Revision as of 12:55, 29 April 2015
Cytochrome c with heme complex with sulfate (PDB code 3cp5)
The cytochrome c (cyt c) proteins are a superfamily belonging to the class of all-α proteins, which are denoted as such by having an α-helical core. Each protein in this superfamily also contains one or more covalently-bound heme prosthetic groups.[1][2] The cyt c superfamily contains many different families, some of which are better characterized than others. These families include monodomain and multi-domain C-type cytochromes, such as cyt c4, a diheme C-type cytochrome, and NrfB, a pentaheme C-type cytochrome. In particular, the monoheme cyt c from Rhodothermus marinus has been previously studied and provides an excellent example of how some protein characteristics and structures can be extremely diverse, yet conserved, through evolution. For details on decaheme cyt see MtrF.
Cytochromes are a class of heme-containing proteins found in bacteria and the mitochondria of eukaryotes.[2] These proteins are generally membrane-bound and are known as respiratory pigments because they are involved in various electron transport systems in oxidative phosphorylation.[3] Cytochromes can be categorized into several different types, three of which are based on the type of heme group the cytochrome contains: cytochromes a, b and d contain heme a, b and d, respectively.[4] Cytochrome c is named such because it contains the heme c, but is mainly distinguished from cytochromes a, b and d due to the heme being coordinated with the protein scaffold by cysteinyl residues covalently bound to either one or both of the heme's vinyl side chains.[3]
Cyt c has been split into four classes.[4] Class I contains soluble, low spin[2] single domain C-type cytochromes, of which there has been at least six subclasses found in prokaryotes including Desulfovibrio desulfuricans, Rhodospirillum rubrum, and Rhodothermus marinus. Cyt c in this class have a single heme attached close to the N-terminus of the polypeptide, with a methionine residue being the sixth iron coordination site. Class II contains higher spin-state cytochromes c, such as cyt c', with the heme being attached closer to the C-terminus. Class III contains cytochromes with multiple heme groups; these proteins have lower redox potentials compared to the other three classes[4]. Finally, Class IV is comprised of more complex proteins with higher molecular weights containing heme c as well as other prosthetic groups.[5]
All members in the C-type cytochrome superfamily contain a heme prosthetic group that is covalently attached to the protein via two thioether bonds to cysteine residues. Most cytochromes c occur in a CXXCH motif where the histidine residue is one of the two axial ligands of the heme iron.[2][3] In monoheme cytochromes c, the other axial position may be left vacant or be occupied by histidine or methionine residues; however, it can sometimes be occupied by cysteine or lysine residues.[2]. In Rmcytc, XX represents a threonine (Thr46) and an alanine residue (Ala47) that help form the loop 2 structure.
Figure 2. The tetrapyrrolic heme prosthetic group that can either be covalently attached to or closely associated with various proteins, such as cytochromes and other globin proteins. In Rmcytc, R2 is an ethyl group covalently attached to Cys 45, and R3 is a methyl group covalently attached to Cys48.
The typical monoheme cyt c fold is formed by helices A, C, and E. Rmcytc contains seven α-helices that are folded around the heme, all connected by random coils.[2] The heme group is axially coordinated by His49 and Met100, and the disulfide linkages exist at Cys45 and Cys48. The heme group in Rmcytc is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes c. First, a 21 amino acid extension of the N-terminal exists, forming α-helix A' and loop 1, which wraps around the back of the polypeptide.[2] An extension resembling such has only been seen in Thermus thermophilus; however, the extension occurs at the C-terminus rather than the N-terminus.[6] A second rarity is that of helix B', inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.[2] In cytochrome c2 as well as mitochondrial cyt c, a similar yet shorter helix was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', T. thermophilus contains a two-stranded β-sheet.[2] One final note is the number of methionine residues that Rmcytc contains. In general, cyt c contains about two methionines whereas Rmcytc contains seven, located on the left of the heme.[2]
As determined by X-ray crystallography, the Rmcytc structure was found to contain a sulfate ion coordinated to Glu122 via hydrogen bonding to the protonated carboxylate oxygen. In the protein complex, this ion has been seen to mediate crystal contact between neighbouring protein molecules.[2]
The observation of these structural motifs in other C-type cytochromes can support the divergent evolution of cytochromes c.[2] These motifs are present in a number of different bacteria and are seen in similar regions of the secondary structure; however, they exist in the primary sequence in places distinct to the phylum. For example, monoheme cytochromes c in the rest of the Bacteroidetes phylum have an N-terminus extension that is highly conserved to that of Rmcytc, and the regions in the primary structure that correspond to these secondary motifs are not observed in other bacterial phyla.[2] Also, due to these motifs being absent from other phyla, the Bacteroidetes monoheme cyt c has been said to form a new subfamily of cyt c.
Function
Monoheme cytochromes c are involved in electron transport chains in both prokaryotes and eukaryotic mitochondria.[2] They mediate the transfer of electrons mainly from the bc1 complexes or their analogs to heme-copper oxygen reductases (HCOs) in the electron transport chain of oxidative phosphorylation. Heme c containing domains are often found fused to other protein domains such as these HCOs, including the caa3 oxygen reductases[2][7]; these enzymes are membrane-bound and catalyze the reduction of O2 to water.[8] In addition to being involved in oxidative phosphorylation, monoheme cyt c has also been seen to participate in the electron transport chain of photosynthesis.[2] Cytochrome c has also been determined to be a major signalling molecule in the apoptotic pathways.
Electron transport chain
In the electron transport chain (ETC), cyt c shuttles electrons between the respiratory complexes III and IV; complex III is the cytochrome bc1 complex and IV is cyt c oxidase. Initially, the heme iron in cyt c is in the reduced, Fe3+ state; this allows for the uptake of one electron, oxidizing the iron to the Fe2+ state.[9] The ETC in eukaryotes is quite simple compared to that of prokaryotes (Figure 3).
Figure 3. The electron transport chain of a) eukaryotes as compared to b) prokaryotes.
In prokaryotic systems, electrons can enter the ETC at a number of places and multiple donors can be in play; however, the underlying transport system remains the same. Electrons are ultimately transferred from donor to various redox complexes including the bc1 complex and cytochrome c, and finally to a terminal electron acceptor such as molecular oxygen in eukaryotes.[9]
The cytochrome oxidase reaction accounts for nearly 90% of all oxygen uptake in most cells.[9] Due to the large role of cytochromes within the ETC, it would be highly detrimental to the cell if any inhibitors were to be present in the organism. Cyanide and azide bind tightly to the cytochrome oxidase complex, halting electron transport and reducing the overall ATP production.[9]
Apoptosis
In all organisms, cells undergo apoptosis, or programmed cell death, by which there is an extrinsic and an intrinsic pathway. The extrinsic pathway involves an immune response by killer lymphocytes, and once the lymphocyte has been bound to the target cell, an apoptotic cascade occurs.[9] The intrinsic pathway includes cyt c, present in the intermembrane space of mitochondria. In this pathway, the presence of an apoptotic stimulus causes cyt c to be released into the cytosol. Cytochrome c in the cytosol now can be recognized and bound to various apoptotic factors, activating them and forming the apoptosome. The apoptosome recruits caspases, which are activated and result in a caspase cascade to proceed with apoptosis.[9]
Cytochrome c is required for the intrinsic apoptotic process to function properly. Such as with the electron transport chain, a mutation affecting cyt c or other structures in apoptosis could cause either an increase or a decrease in the rate of apoptosis.
Structural and kinetic studies of imidazole binding to two members of the cytochrome c6 family reveal an important role for a conserved heme pocket residue[10]
Cytochrome c6 is a member of the class I family of c-type cytochromes with a distinctive α-helical fold and a methionine and histidine residue serving as axial heme iron ligands. They function in the photosynthetic electron transport chain of cyanobacteria where they shuttle an electron from the cytochrome b6f complex to photosystem I. Structures of numerous cytochrome c6 proteins have been determined and all have the methionine ligand coordinating to the iron. In the present work we have solved the structure of the Q51V site-directed variant of Phormidium laminosum cytochrome c6. This project is part of a study that is aimed at gaining insight into protein factors which modulate the heme mid-point redox potential in the cytochrome c6 family. The Q51V variant has been shown to tune over 100 mV of heme redox potential, which for a single heme pocket mutation is very significant and has consequences for function.
Structural model of the [Fe]-hydrogenase/cytochrome C553 complex combining NMR and soft-docking[11]
The complex shows the specific interaction of the hydrogenase (light blue) with the cytochrome (pink), revealing the path of electron transport from the active site metal cluster, through three iron-sulfur clusters, and ending in the cytochrome heme (colored red). Two cysteine amino acids at the interface, CYS 38 in the hydrogenase and CYS10 in the cytochrome, are thought to provide the electron transfer pathway between the two proteins (these scenes were created by Jaime Prilusky, David S. Goodsell, and Eran Hodis).
↑Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001 Nov 2;313(4):903-19. PMID:11697912 doi:10.1006/jmbi.2001.5080
↑ 2.002.012.022.032.042.052.062.072.082.092.102.112.122.132.142.15Stelter M, Melo AM, Pereira MM, Gomes CM, Hreggvidsson GO, Hjorleifsdottir S, Saraiva LM, Teixeira M, Archer M. A Novel Type of Monoheme Cytochrome c: Biochemical and Structural Characterization at 1.23 A Resolution of Rhodothermus marinus Cytochrome c. Biochemistry. 2008 Oct 15. PMID:18855424 doi:10.1021/bi800999g
↑ 4.04.14.2Ambler RP. Sequence variability in bacterial cytochromes c. Biochim Biophys Acta. 1991 May 23;1058(1):42-7. PMID:1646017
↑Cookson DJ, Moore GR, Pitt RC, Williams RJP, Campbell ID, Ambler RP, Bruschi M, Le Gall J. Structural homology of cytochromes c. Eur J Biochem. 1978 Feb;83(1):261-75.
↑Than ME, Hof P, Huber R, Bourenkov GP, Bartunik HD, Buse G, Soulimane T. Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing. J Mol Biol. 1997 Aug 29;271(4):629-44. PMID:9281430 doi:10.1006/jmbi.1997.1181
↑Soares CM, Baptista AM, Pereira MM, Teixeira M. Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase. J Biol Inorg Chem. 2004 Mar;9(2):124-34. Epub 2003 Dec 23. PMID:14691678 doi:10.1007/s00775-003-0509-9
↑Pereira MM, Santana M, Teixeira M. A novel scenario for the evolution of haem-copper oxygen reductases. Biochim Biophys Acta. 2001 Jun 1;1505(2-3):185-208. PMID:11334784
↑ 9.09.19.29.39.49.5Karp, Gerald (2008). Cell and Molecular Biology (5th edition). Hoboken, NJ: John Wiley & Sons. ISBN 978-0470042175.
↑Rajagopal BS, Wilson MT, Bendall DS, Howe CJ, Worrall JA. Structural and kinetic studies of imidazole binding to two members of the cytochrome c (6) family reveal an important role for a conserved heme pocket residue. J Biol Inorg Chem. 2011 Jan 26. PMID:21267610 doi:10.1007/s00775-011-0758-y
↑Morelli X, Czjzek M, Hatchikian CE, Bornet O, Fontecilla-Camps JC, Palma NP, Moura JJ, Guerlesquin F. Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem. 2000 Jul 28;275(30):23204-10. PMID:10748163 doi:10.1074/jbc.M909835199
