P00044 (CYC1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cytochrome c iso-1

Gene names

Name:	CYC1
Ordered Locus Names:	YJR048W
ORF Names:	J1653

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	109 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
Subcellular location	Mitochondrion intermembrane space. Note: Loosely associated with the inner membrane By similarity.
Developmental stage	Iso-1 is the predominant cytochrome c in aerobically grown cells.
Induction	By oxygen.
Post-translational modification	Binds 1 heme group per subunit. Methylation may enhance its transport into mitochondria. Methylation occurs in fungi, plants, and some protozoa, but not in animals. The precise role of methylation at Lys-79 is unknown, but it seems to preclude pro-apoptotic activity, possibly by lowering affinity for APAF1. Ref.10 Ref.11 Ref.12 Ref.19
Miscellaneous	Present with 7330 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the cytochrome c family.

Ontologies

Keywords
Biological process	Electron transport Respiratory chain Transport
Cellular component	Mitochondrion
Ligand	Heme Iron Metal-binding
PTM	Methylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	mitochondrial electron transport, cytochrome c to oxygen Inferred from direct assay PubMed 7851399. Source: SGD mitochondrial electron transport, ubiquinol to cytochrome c Inferred from direct assay PubMed 7851399. Source: SGD
Cellular_component	mitochondrial intermembrane space Inferred from direct assay PubMed 9866716. Source: SGD respiratory chain Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	electron carrier activity Inferred from direct assay PubMed 18975895PubMed 7851399. Source: SGD heme binding Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CCP1	P00431	2	EBI-5393,EBI-4389

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7

Chain

2 – 109

108

Cytochrome c iso-1

PRO_0000108337

Sites

Metal binding

24

1

Iron (heme axial ligand)

Metal binding

86

1

Iron (heme axial ligand)

Binding site

20

1

Heme (covalent)

Binding site

23

1

Heme (covalent)

Amino acid modifications

Modified residue

78

1

N6,N6,N6-trimethyllysine; by CTM1 Ref.12

Modified residue

79

1

N6,N6,N6-trimethyllysine Ref.11 Ref.19

Experimental info

Mutagenesis

78

1

K → R: Loss of methylation by CTM1. Ref.12

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

109

Helix Strand Turn

Details...

Helix

9 – 19

11

Turn

20 – 23

4

Beta strand

27 – 29

3

Beta strand

33 – 35

3

Turn

39 – 43

5

Beta strand

45 – 47

3

Beta strand

50 – 52

3

Helix

56 – 61

6

Helix

67 – 75

9

Helix

77 – 80

4

Beta strand

81 – 83

3

Helix

94 – 107

14

Sequences

	Sequence		Length	Mass (Da)
	P00044 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 1F8B6CB3B60C0BE8	FASTA	109	12,182
	10 20 30 40 50 60 MTEFKAGSAK KGATLFKTRC LQCHTVEKGG PHKVGPNLHG IFGRHSGQAE GYSYTDANIK 70 80 90 100 KNVLWDENNM SEYLTNPKKY IPGTKMAFGG LKKEKDRNDL ITYLKKACE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae." Smith M., Leung D.W., Gillam S., Astell C.R., Montgomery D.L., Hall B.D. Cell 16:753-761(1979) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Sequence of the yeast iso-1-cytochrome c mRNA." Boss J.M., Gillam S., Ziotmer R.S., Smith M. J. Biol. Chem. 256:12958-12961(1981) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"Nucleotide sequence of the COR region: a cluster of six genes in the yeast Saccharomyces cerevisiae." Melnick L., Sherman F. Gene 87:157-166(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Revised nucleotide sequence of the COR region of yeast Saccharomyces cerevisiae chromosome X." Huang M.-E., Manus V., Chuat J.-C., Galibert F. Yeast 10:811-818(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X." Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[7]	"The complete amino acid sequence in baker's yeast cytochrome c." Narita K., Titani K. J. Biochem. 65:259-267(1969) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-109. Strain: Oviformis.
[8]	"Transcription initiation of the Saccharomyces cerevisiae iso-1-cytochrome c gene. Multiple, independent T-A-T-A sequences." McNeil J.B., Smith M. J. Mol. Biol. 187:363-378(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[9]	"Studies on cytochrome c. 8. Synthesis of the protected hexadecapeptide (sequence 93-108) of Baker's yeast iso-1-cytochrome c." Moroder L., Marchiori F., Borin G., Scoffone E. Biopolymers 12:729-750(1973) [PubMed] [Europe PMC] [Abstract] Cited for: SYNTHESIS.
[10]	"Enzymatic methylation of in vitro synthesized apocytochrome c enhances its transport into mitochondria." Park K.S., Frost B., Tuck M., Ho L.L., Kim S., Paik W.K. J. Biol. Chem. 262:14702-14708(1987) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION.
[11]	"Determinants of cytochrome c pro-apoptotic activity. The role of lysine 72 trimethylation." Kluck R.M., Ellerby L.M., Ellerby H.M., Naiem S., Yaffe M.P., Margoliash E., Bredesen D., Mauk A.G., Sherman F., Newmeyer D.D. J. Biol. Chem. 275:16127-16133(2000) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-79.
[12]	"Cytochrome c methyltransferase, Ctm1p, of yeast." Polevoda B., Martzen M.R., Das B., Phizicky E.M., Sherman F. J. Biol. Chem. 275:20508-20513(2000) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-78, MUTAGENESIS OF LYS-78.
[13]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]	"Yeast iso-1-cytochrome c. A 2.8-A resolution three-dimensional structure determination." Louie G.V., Hutcheon W.L., Brayer G.D. J. Mol. Biol. 199:295-314(1988) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[15]	"High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c." Louie G.V., Brayer G.D. J. Mol. Biol. 214:527-555(1990) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.23 ANGSTROMS).
[16]	"Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c." Lange C., Hunte C. Proc. Natl. Acad. Sci. U.S.A. 99:2800-2805(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.97 ANGSTROMS).
[17]	"Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c." Baistrocchi P., Banci L., Bertini I., Turano P., Bren K.L., Gray H.B. Biochemistry 35:13788-13796(1996) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
[18]	"Solution structure of oxidized Saccharomyces cerevisiae iso-1-cytochrome c." Banci L., Bertini I., Bren K.L., Gray H.B., Sompornpisut P., Turano P. Biochemistry 36:8992-9001(1997) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
[19]	"Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer." Solmaz S.R., Hunte C. J. Biol. Chem. 283:17542-17549(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-109 IN THE BC1 COMPLEX, METHYLATION AT LYS-79.
+	Additional computationally mapped references.

Web resources

Protein Spotlight

Life shuttle - Issue 76 of November 2006

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M37696 Genomic DNA. Translation: AAB59344.1.
V01298 Genomic DNA. Translation: CAA24605.1.
L26347 Genomic DNA. Translation: AAA62856.1.
L36344 Genomic DNA. Translation: AAA88751.1.
Z49548 Genomic DNA. Translation: CAA89576.1.
X03472 Genomic DNA. Translation: CAA27189.1.
BK006943 Genomic DNA. Translation: DAA08835.1.

PIR

CCBY. A00037.

RefSeq

NP_012582.1. NM_001181706.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CHH	X-ray	1.97	A	2-107	[»]
1CHI	X-ray	2.00	A	2-107	[»]
1CHJ	X-ray	1.90	A	2-107	[»]
1CIE	X-ray	1.80	A	2-107	[»]
1CIF	X-ray	1.90	A	2-107	[»]
1CIG	X-ray	1.80	A	2-107	[»]
1CIH	X-ray	1.80	A	2-107	[»]
1CRG	X-ray	2.00	A	2-107	[»]
1CRH	X-ray	1.90	A	2-108	[»]
1CRI	X-ray	2.00	A	2-107	[»]
1CRJ	X-ray	2.05	A	2-107	[»]
1CSU	X-ray	1.81	A	2-107	[»]
1CSV	X-ray	1.90	A	2-107	[»]
1CSW	X-ray	1.90	A	2-107	[»]
1CSX	X-ray	1.90	A	2-107	[»]
1CTY	X-ray	2.20	A	2-107	[»]
1CTZ	X-ray	1.90	A	2-107	[»]
1FHB	NMR	-	A	2-107	[»]
1IRV	X-ray	1.90	A	2-107	[»]
1IRW	X-ray	2.00	A	2-107	[»]
1KYO	X-ray	2.97	W	2-109	[»]
1LMS	NMR	-	A	2-107	[»]
1NMI	NMR	-	A	2-107	[»]
1RAP	X-ray	2.25	A	2-108	[»]
1RAQ	X-ray	1.90	A	2-108	[»]
1S6V	X-ray	1.88	B/D	3-107	[»]
1U74	X-ray	2.40	B/D	2-107	[»]
1YCC	X-ray	1.23	A	2-109	[»]
1YFC	NMR	-	A	2-107	[»]
1YIC	NMR	-	A	2-107	[»]
2B0Z	X-ray	2.70	B	2-108	[»]
2B10	X-ray	2.80	B/D	2-109	[»]
2B11	X-ray	2.30	B/D	2-108	[»]
2B12	X-ray	3.02	B	2-108	[»]
2BCN	X-ray	1.70	B	2-107	[»]
2GB8	NMR	-	B	2-108	[»]
2HV4	NMR	-	A	2-107	[»]
2JQR	NMR	-	A	2-107	[»]
2JTI	NMR	-	B	2-109	[»]
2LIR	NMR	-	A	2-107	[»]
2LIT	NMR	-	A	2-107	[»]
2ORL	NMR	-	A	2-107	[»]
2PCC	X-ray	2.30	B/D	2-108	[»]
2YCC	X-ray	1.90	A	2-107	[»]
3CX5	X-ray	1.90	W	2-109	[»]
3TYI	X-ray	1.40	A/B	2-107	[»]

ProteinModelPortal

P00044.

SMR

P00044. Positions 2-109.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4265N.

IntAct

P00044. 4 interactions.

MINT

MINT-509316.

STRING

4932.YJR048W.

Proteomic databases

PaxDb

P00044.

PeptideAtlas

P00044.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YJR048W; YJR048W; YJR048W.

GeneID

853507.

KEGG

sce:YJR048W.

Organism-specific databases

SGD

S000003809. CYC1.

Phylogenomic databases

eggNOG

COG3474.

GeneTree

ENSGT00390000009405.

HOGENOM

HOG000009762.

KO

K08738.

OMA

KMIYAGL.

OrthoDB

EOG469V49.

Gene expression databases

ArrayExpress

P00044.

Genevestigator

P00044.

GermOnline

YJR048W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002327. Cyt_c_1A/1B.
IPR009056. Cyt_c_dom.
IPR003088. Cyt_c_I.
[Graphical view]

PANTHER

PTHR11961. PTHR11961. 1 hit.

Pfam

PF00034. Cytochrom_C. 1 hit.
[Graphical view]

PRINTS

PR00604. CYTCHRMECIAB.

SUPFAM

SSF46626. Cytochrome_c. 1 hit.

PROSITE

PS51007. CYTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00044.

NextBio

974162.

Entry information

Entry name

CYC1_YEAST

Accession

Primary (citable) accession number: P00044
Secondary accession number(s): D6VWL9

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 155 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program