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Sandbox Reserved 335

This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
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PDB ID 3cp5

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3cp5, resolution 1.24Å ()
Ligands: ,
Gene: cytC (Rhodothermus marinus)
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


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.

IntroductionIntroduction

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]

Rhodothermus marinus cytochrome cRhodothermus marinus cytochrome c

StructureStructure

Figure 1. The heme group of monoheme cytochrome

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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 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 . Rmcytc contains seven α-helices that are folded around the heme, all connected by random coils.[2] The heme group is axially coordinated by , and the disulfide linkages exist at . 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 , 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 , 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 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.

FunctionFunction

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]

In addition to being involved in the electron transfer in many systems, cyt c is involved in cell apoptosis, the programmed death of a cell due to cellular signals. Cyt c is

Electron transport chainElectron 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.

ApoptosisApoptosis

ImportanceImportance

C-type cytochromes are required for the apoptotic and electron transfer processes to function properly.[10]

ReferencesReferences

  1. ↑ 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. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 2.15 Stelter 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
  3. ↑ 3.0 3.1 3.2 Reedy CJ, Gibney BR. Heme protein assemblies. Chem Rev. 2004 Feb;104(2):617-49. PMID:14871137 doi:10.1021/cr0206115
  4. ↑ 4.0 4.1 4.2 Ambler RP. Sequence variability in bacterial cytochromes c. Biochim Biophys Acta. 1991 May 23;1058(1):42-7. PMID:1646017
  5. ↑ 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.
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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. ↑ ISBN:10-0-470-04217-6
  10. ↑ doi:10.1038/ng.103

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