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词条 Cytochrome c family
释义

  1. Classification

      Class I   Subclasses   Class II    Class III    Class IV  

  2. Biogenesis

      System I    System II    System III    System IV  

  3. Human proteins containing this domain

  4. References

Cytochromes c (cyt c, c-type cytochromes) are proteins containing one or more heme groups that are covalently attached to the peptide backbone via one or two thioether bonds.[1] These bonds are in most cases part of a specific Cys-X-X-Cys-His (CXXCH) binding motif, where X denotes a miscellaneous amino acid. Two thioether bonds of cysteine residues bind to the vinyl sidechains of heme, and the histidine residue coordinates one axial binding site of the heme iron. Less common binding motifs can include a single thioether linkage,[2] a lysine[3] or a methionine[4] instead of the axial histidine or a CXnCH binding motif with n>2.[5] The second axial site of the iron can be coordinated by amino acids of the protein,[6] substrate molecules or water. Cytochromes c possess a wide range of properties and function as electron transfer proteins or catalyse chemical reactions involving redox processes.[7] A prominent member of this family is mitochondrial cytochrome c.

Classification

{{Infobox protein
| name = Class I example: Cytochrome c
| AltNames =
| image = PDB_1cry_EBI.jpg
| width =
| caption = Structure of cytochrome c2 from Rhodopseudomonas viridis.[8]
| Symbol = Cytochrom_C
| AltSymbols =
| IUPHAR_id =
| ATC_prefix =
| ATC_suffix =
| ATC_supplemental =
| CAS_number =
| CAS_supplemental =
| DrugBank =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB = 1cry
| RefSeq =
| UniProt = P00083
| EC_number =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}{{Infobox protein
| name = Class II example: Cytochrome c'
| AltNames =
| image = PDB 1bbh EBI.jpg
| width =
| caption = Atomic structure of a cytochrome c' dimer.
| Symbol = Cytochrom_C_2
| AltSymbols =
| IUPHAR_id =
| ATC_prefix =
| ATC_suffix =
| ATC_supplemental =
| CAS_number =
| CAS_supplemental =
| DrugBank =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB = 1cgo
| RefSeq =
| UniProt = P00138
| EC_number =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}{{Infobox protein
| name = Class III example: High molecular weight cytochrome c
| AltNames =
| image = PDB 1h29 EBI.jpg
| width =
| caption = Structure of the 16-heme cytochrome c Hmc from Desulfovibrio vulgaris hildenborough.
| Symbol = Cytochrom_CIII
| AltSymbols =
| IUPHAR_id =
| ATC_prefix =
| ATC_suffix =
| ATC_supplemental =
| CAS_number =
| CAS_supplemental =
| DrugBank =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB = 2cdv
| RefSeq =
| UniProt = P00132
| EC_number =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}{{Infobox protein
| name = Class IV example: Flavocytochrome c sulfide dehydrogenase
| AltNames =
| image = PDB 1fcd EBI.jpg
| width =
| caption = Structure of the flavocytochrome c sulfide dehydrogenase from the purple phototrophic bacterium Chromatium vinosum.
| Symbol = FCSD-flav_bind
| AltSymbols =
| IUPHAR_id =
| ATC_prefix =
| ATC_suffix =
| ATC_supplemental =
| CAS_number =
| CAS_supplemental =
| DrugBank =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB = 1fcd
| RefSeq =
| UniProt = Q06530
| EC_number =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}

Cytochrome c proteins can be divided in four classes[9] based on their size, number of heme groups and reduction potentials:

Class I

Small soluble cytochrome c proteins with a molecular weight of 8-12 kDa and a single heme group belong to class I.[10][11] It includes the low-spin soluble cytC of mitochondria and bacteria, with the heme-attachment site located towards the N-terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C-terminus. The typical class I fold contains five α-helices. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cyt c and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c550, which have several extra loops by comparison with class IB cyt c.

Subclasses

  • Cytochrome c, class IA/ IB {{InterPro|IPR002327}}
  • Cytochrome c, class IC {{InterPro|IPR008168}}
  • Cytochrome c, class ID {{InterPro|IPR002324}}
  • Cytochrome c, class IE {{InterPro|IPR002323}}

Class II

The heme group in class II cytochrome c proteins is attached to a C-terminal binding motif. The structural fold of class II c-type cytochromes contains a four α-helix bundle with the covalently attached heme group at its core.[12] Representatives of class II are the high-spin cytochrome c' and a number of low-spin cytochromes c, e.g. cyt c556. The cyt c' are capable of binding such ligands as CO, NO or CN-, albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin hemeproteins.[12] This, coupled with its relatively low redox potential, makes it unlikely that cyt c' is a terminal oxidase. Thus cyt c' probably functions as an electron transfer protein.[13] The 3D structures of a number of cyt c' have been determined which show that the proteins usually exist as a dimer. The Chromatium vinosum cyt c' exhibits dimer dissociation upon ligand binding.[14]

Class III

Proteins containing multiple covalently attached heme groups with low redox potential are included in class III. The heme C groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV.[15] Members of this class are e.g. cytochrome c7 (triheme), cytochrome c3 (tetraheme), and high-molecular-weight cytochrome c (Hmc), cointaining 16 heme groups with only 30-40 residues per heme group.[16] The 3D structures of a number of cyt c3 proteins have been determined. The proteins consist of 4-5 α-helices and 2 β-sheets wrapped around a compact core of four non-parallel hemes, which present a relatively high degree of exposure to the solvent. The overall protein architecture, heme plane orientations and iron-iron distances are highly conserved.[15]

Class IV

Cytochrome c proteins containing other prosthetic groups besides heme C, such as flavocytochromes c and cytochromes cd belong to class IV.[9] An example is the photosynthetic reaction center of Rhodopseudomonas viridis that contains a tetraheme cytochrome c subunit.[17]

Biogenesis

The attachment of the heme group is physically separated from the protein biosynthesis. Proteins are synthesized within the cytoplasm and endoplasmic reticulum, while the maturation of cytochromes c occurs in the periplasm of prokaryots, the intermembrane space of mitochondria or the stroma of chloroplasts. Several biochemical pathways have been discovered that differ depending on organism.[18]

System I

Also called cytochrome c maturation (ccm)[19] and found in proteobacteria, plant mitochondria, some protozoal mitochondria, deinococci and archaea. Ccm comprises at least eight membrane proteins (CcmABCDEFGH) that are needed for electron transfer to the heme group, apo-cytochrome handling and attachment of the heme to the apo-cytochrome. An ABC-transporter-like complex formed by CcmA2BCD attaches a heme group to CcmE with the use of ATP. CcmE transports the heme to CcmF where the attachment to the apo-cytochrome occurs. Transport of the apoprotein from the cytoplasm to the periplasm happens via the Sec translocation system. CcmH is used by the system to recognize the apo-cytochrome and direct it to CcmF.

System II

Cytochromes c in chloroplasts, Gram-positive bacteria, cyanobacteria and some proteobacteria are produced by the cytochrome c synthesis (ccs) system. It is comprised of two membrane proteins CcsB and CcsA. The CcsBA protein complex was suggested to act as a heme transporter during the attachment process.[20] In some organisms such as Helicobacter hepaticus both proteins are found as a fused single protein. Apoprotein transport occurs via the Sec translocon as well.

System III

Fungal, vertebrate and invertebrate mitochondria produce cytochrome c proteins with a single enzyme called HCCS (holocytochrome c synthase) or cytochrome c heme lyase (CCHL).[21][22] The protein is attached to the inner membrane of the intermembrane space.[23] In some organisms, such as Saccharomyces cerevisiae, cytochrome c and cytochrome c1 are synthesized by separate heme lyases, CCHL and CC1HL respectively.[24] In Homo sapiens a single HCCS is used for the biosynthesis of both cytochrome c proteins.[25]

System IV

Four membrane proteins are necessary for the attachment of a heme in cytochrome b6. A major difference to systems I-III is that the heme attachment occurs at the opposite side of the lipid bilayer compared to the other systems.[18]

Human proteins containing this domain

CYCS; CYC1

References

1. ^{{cite journal | vauthors = | title = Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Nomenclature of electron-transfer proteins. Recommendations 1989 | journal = The Journal of Biological Chemistry | volume = 267 | issue = 1 | pages = 665–77 | date = January 1992 | pmid = 1309757 }}
2. ^{{cite journal | vauthors = Allen JW, Ginger ML, Ferguson SJ | title = Maturation of the unusual single-cysteine (XXXCH) mitochondrial c-type cytochromes found in trypanosomatids must occur through a novel biogenesis pathway | journal = The Biochemical Journal | volume = 383 | issue = Pt. 3 | pages = 537–42 | date = November 2004 | pmid = 15500440 | pmc = 1133747 | doi = 10.1042/BJ20040832 }}
3. ^{{cite journal | vauthors = Eaves DJ, Grove J, Staudenmann W, James P, Poole RK, White SA, Griffiths I, Cole JA | title = Involvement of products of the nrfEFG genes in the covalent attachment of haem c to a novel cysteine-lysine motif in the cytochrome c552 nitrite reductase from Escherichia coli | journal = Molecular Microbiology | volume = 28 | issue = 1 | pages = 205–16 | date = April 1998 | pmid = 9593308 }}
4. ^{{cite journal | vauthors = Rodrigues ML, Oliveira TF, Pereira IA, Archer M | title = X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination | journal = The EMBO Journal | volume = 25 | issue = 24 | pages = 5951–60 | date = December 2006 | pmid = 17139260 | pmc = 1698886 | doi = 10.1038/sj.emboj.7601439 }}
5. ^{{cite journal | vauthors = Hartshorne RS, Kern M, Meyer B, Clarke TA, Karas M, Richardson DJ, Simon J | title = A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding | journal = Molecular Microbiology | volume = 64 | issue = 4 | pages = 1049–60 | date = May 2007 | pmid = 17501927 | doi = 10.1111/j.1365-2958.2007.05712.x }}
6. ^{{cite journal | vauthors = Assfalg M, Bertini I, Dolfi A, Turano P, Mauk AG, Rosell FI, Gray HB | title = Structural model for an alkaline form of ferricytochrome C | journal = Journal of the American Chemical Society | volume = 125 | issue = 10 | pages = 2913–22 | date = March 2003 | pmid = 12617658 | doi = 10.1021/ja027180s }}
7. ^{{cite book |last1=Pettigrew |first1=Graham W. |last2=Moore |first2=Geoffrey R. |name-list-format=vanc |title=Cytochromes c : Biological Aspects |date=1987 |publisher=Springer |location=Berlin Heidelberg |isbn=978-3-642-72698-9 |pages=113–229 |chapter=The Function of Bacterial and Photosynthetic Cytochromes c|doi=10.1007/978-3-642-72698-9_3}}
8. ^{{cite journal | vauthors = Miki K, Sogabe S, Uno A, Ezoe T, Kasai N, Saeda M, Matsuura Y, Miki M | title = Application of an automatic molecular-replacement procedure to crystal structure analysis of cytochrome c2 from Rhodopseudomonas viridis | journal = Acta Crystallographica Section D | volume = 50 | issue = Pt 3 | pages = 271–5 | date = May 1994 | pmid = 15299438 | doi = 10.1107/S0907444993013952 }}
9. ^1 {{cite journal | vauthors = Ambler RP | title = Sequence variability in bacterial cytochromes c | journal = Biochimica et Biophysica Acta | volume = 1058 | issue = 1 | pages = 42–7 | date = May 1991 | pmid = 1646017 | doi = 10.1016/S0005-2728(05)80266-X }}
10. ^{{cite journal | vauthors = Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y | title = Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers | language = EN | journal = Chemical Reviews | volume = 114 | issue = 8 | pages = 4366–469 | date = April 2014 | pmid = 24758379 | pmc = 4002152 | doi = 10.1021/cr400479b }}
11. ^{{cite journal | vauthors = Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH | title = Multifunctional Cytochrome c: Learning New Tricks from an Old Dog | journal = Chemical Reviews | volume = 117 | issue = 21 | pages = 13382–13460 | date = November 2017 | pmid = 29027792 | doi = 10.1021/acs.chemrev.7b00257 }}
12. ^{{cite journal | vauthors = Kassner RJ | title = Ligand binding properties of cytochromes c' | journal = Biochimica et Biophysica Acta | volume = 1058 | issue = 1 | pages = 8–12 | date = May 1991 | pmid = 1646027 | doi = 10.1016/s0005-2728(05)80257-9 }}
13. ^1 {{cite journal | vauthors = Moore GR | title = Bacterial 4-alpha-helical bundle cytochromes | journal = Biochimica et Biophysica Acta | volume = 1058 | issue = 1 | pages = 38–41 | date = May 1991 | pmid = 1646016 | doi = 10.1016/s0005-2728(05)80265-8 }}
14. ^{{cite journal | vauthors = Ren Z, Meyer T, McRee DE | title = Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution | journal = Journal of Molecular Biology | volume = 234 | issue = 2 | pages = 433–45 | date = November 1993 | pmid = 8230224 | doi = 10.1006/jmbi.1993.1597 }}
15. ^1 {{cite journal | vauthors = Coutinho IB, Xavier AV | title = Tetraheme cytochromes | journal = Methods in Enzymology | volume = 243 | issue = | pages = 119–40 | year = 1994 | pmid = 7830606 | doi = 10.1016/0076-6879(94)43011-X }}
16. ^{{cite journal | vauthors = Czjzek M, ElAntak L, Zamboni V, Morelli X, Dolla A, Guerlesquin F, Bruschi M | title = The crystal structure of the hexadeca-heme cytochrome Hmc and a structural model of its complex with cytochrome c(3) | journal = Structure | volume = 10 | issue = 12 | pages = 1677–86 | date = December 2002 | pmid = 12467575 | doi = 10.1016/s0969-2126(02)00909-7 }}
17. ^{{cite journal | vauthors = Lancaster CR, Hunte C, Kelley J, Trumpower BL, Ditchfield R | title = A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex | journal = Journal of Molecular Biology | volume = 368 | issue = 1 | pages = 197–208 | date = April 2007 | pmid = 17337272 | doi = 10.1016/j.jmb.2007.02.013 }}
18. ^1 {{cite journal | vauthors = Kranz RG, Richard-Fogal C, Taylor JS, Frawley ER | title = Cytochrome c biogenesis: mechanisms for covalent modifications and trafficking of heme and for heme-iron redox control | journal = Microbiology and Molecular Biology Reviews | volume = 73 | issue = 3 | pages = 510–28, Table of Contents | date = September 2009 | pmid = 19721088 | pmc = 2738134 | doi = 10.1128/MMBR.00001-09 }}
19. ^{{cite journal | vauthors = Stevens JM, Mavridou DA, Hamer R, Kritsiligkou P, Goddard AD, Ferguson SJ | title = Cytochrome c biogenesis System I | journal = The FEBS Journal | volume = 278 | issue = 22 | pages = 4170–8 | date = November 2011 | pmid = 21958041 | pmc = 3601427 | doi = 10.1111/j.1742-4658.2011.08376.x }}
20. ^{{cite journal | vauthors = Frawley ER, Kranz RG | title = CcsBA is a cytochrome c synthetase that also functions in heme transport | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 25 | pages = 10201–6 | date = June 2009 | pmid = 19509336 | pmc = 2700922 | doi = 10.1073/pnas.0903132106 }}
21. ^{{cite journal | vauthors = Dumont ME, Ernst JF, Hampsey DM, Sherman F | title = Identification and sequence of the gene encoding cytochrome c heme lyase in the yeast Saccharomyces cerevisiae | journal = The EMBO Journal | volume = 6 | issue = 1 | pages = 235–41 | date = January 1987 | pmid = 3034577 | pmc = 553382 }}
22. ^{{cite journal | vauthors = Hamel P, Corvest V, Giegé P, Bonnard G | title = Biochemical requirements for the maturation of mitochondrial c-type cytochromes | journal = Biochimica et Biophysica Acta | volume = 1793 | issue = 1 | pages = 125–38 | date = January 2009 | pmid = 18655808 | doi = 10.1016/j.bbamcr.2008.06.017 }}
23. ^{{cite journal | vauthors = Babbitt SE, Sutherland MC, San Francisco B, Mendez DL, Kranz RG | title = Mitochondrial cytochrome c biogenesis: no longer an enigma | journal = Trends in Biochemical Sciences | volume = 40 | issue = 8 | pages = 446–55 | date = August 2015 | pmid = 26073510 | pmc = 4509832 | doi = 10.1016/j.tibs.2015.05.006 }}
24. ^{{cite journal | vauthors = Steiner H, Zollner A, Haid A, Neupert W, Lill R | title = Biogenesis of mitochondrial heme lyases in yeast. Import and folding in the intermembrane space | journal = The Journal of Biological Chemistry | volume = 270 | issue = 39 | pages = 22842–9 | date = September 1995 | pmid = 7559417 }}
25. ^{{cite journal | vauthors = Bernard DG, Gabilly ST, Dujardin G, Merchant S, Hamel PP | title = Overlapping specificities of the mitochondrial cytochrome c and c1 heme lyases | journal = The Journal of Biological Chemistry | volume = 278 | issue = 50 | pages = 49732–42 | date = December 2003 | pmid = 14514677 | doi = 10.1074/jbc.M308881200 }}
{{InterPro content|IPR002321}}{{InterPro content|IPR020942}}

2 : Protein domains|Peripheral membrane proteins
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