CYC_ORYSJ
ID CYC_ORYSJ Reviewed; 112 AA.
AC Q0DI31; B7E4T8; P00055; Q6L4Z1;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Cytochrome c;
GN Name=CC-1; OrderedLocusNames=Os05g0420600, LOC_Os05g34770;
GN ORFNames=OsJ_017825, OsJ_18585 {ECO:0000312|EMBL:EEE63765.1},
GN OSJNBb0092E21.3, P0426G01.18;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Yamahoushi;
RA Nishi R., Uchimiya H., Kato A.;
RT "cDNA cloning and sequence analysis of rice cytochrome c gene.";
RL Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP PROTEIN SEQUENCE OF 2-112, ACETYLATION AT ALA-2, AND METHYLATION AT LYS-81
RP AND LYS-95.
RX PubMed=6244261; DOI=10.1093/oxfordjournals.jbchem.a132732;
RA Mori E., Morita Y.;
RT "Amino acid sequence of cytochrome c from rice.";
RL J. Biochem. 87:249-266(1980).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=6304326; DOI=10.1016/s0022-2836(83)80092-8;
RA Ochi H., Hata Y., Tanaka N., Kakudo M., Sakurai T., Aihara S., Morita Y.;
RT "Structure of rice ferricytochrome c at 2.0-A resolution.";
RL J. Mol. Biol. 166:407-418(1983).
CC -!- FUNCTION: Electron carrier protein. The oxidized form of the cytochrome
CC c heme group can accept an electron from the heme group of the
CC cytochrome c1 subunit of cytochrome reductase. Cytochrome c then
CC transfers this electron to the cytochrome oxidase complex, the final
CC protein carrier in the mitochondrial electron-transport chain.
CC -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space. Note=Loosely
CC associated with the inner membrane.
CC -!- PTM: Binds 1 heme c group covalently per subunit.
CC -!- SIMILARITY: Belongs to the cytochrome c family. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Protein Spotlight; Note=Life shuttle - Issue 76 of
CC November 2006;
CC URL="https://web.expasy.org/spotlight/back_issues/076";
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DR EMBL; D12634; BAA02159.1; -; mRNA.
DR EMBL; AC124836; AAT44244.1; -; Genomic_DNA.
DR EMBL; AC137623; AAV25652.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF17492.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS94074.1; -; Genomic_DNA.
DR EMBL; CM000142; EAZ34342.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE63765.1; -; Genomic_DNA.
DR EMBL; AK060267; BAG87385.1; -; mRNA.
DR PIR; JS0709; CCRZ.
DR RefSeq; XP_015640631.1; XM_015785145.1.
DR PDB; 1CCR; X-ray; 1.50 A; A=2-112.
DR PDBsum; 1CCR; -.
DR AlphaFoldDB; Q0DI31; -.
DR SMR; Q0DI31; -.
DR STRING; 4530.OS05T0420600-01; -.
DR iPTMnet; Q0DI31; -.
DR PaxDb; Q0DI31; -.
DR PRIDE; Q0DI31; -.
DR EnsemblPlants; Os05t0420600-01; Os05t0420600-01; Os05g0420600.
DR GeneID; 4338825; -.
DR Gramene; Os05t0420600-01; Os05t0420600-01; Os05g0420600.
DR KEGG; osa:4338825; -.
DR eggNOG; KOG3453; Eukaryota.
DR HOGENOM; CLU_060944_3_0_1; -.
DR InParanoid; Q0DI31; -.
DR OMA; AQCHTIN; -.
DR OrthoDB; 1533604at2759; -.
DR EvolutionaryTrace; Q0DI31; -.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; Q0DI31; OS.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IBA:GO_Central.
DR GO; GO:0070469; C:respirasome; IEA:UniProtKB-KW.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IBA:GO_Central.
DR GO; GO:0006122; P:mitochondrial electron transport, ubiquinol to cytochrome c; IBA:GO_Central.
DR Gene3D; 1.10.760.10; -; 1.
DR InterPro; IPR009056; Cyt_c-like_dom.
DR InterPro; IPR036909; Cyt_c-like_dom_sf.
DR InterPro; IPR002327; Cyt_c_1A/1B.
DR PANTHER; PTHR11961; PTHR11961; 1.
DR Pfam; PF00034; Cytochrom_C; 1.
DR PRINTS; PR00604; CYTCHRMECIAB.
DR SUPFAM; SSF46626; SSF46626; 1.
DR PROSITE; PS51007; CYTC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; Electron transport;
KW Heme; Iron; Metal-binding; Methylation; Mitochondrion; Reference proteome;
KW Respiratory chain; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:6244261"
FT CHAIN 2..112
FT /note="Cytochrome c"
FT /id="PRO_0000108303"
FT BINDING 23
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT BINDING 26
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT BINDING 27
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 89
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000269|PubMed:6244261"
FT MOD_RES 81
FT /note="N6,N6,N6-trimethyllysine"
FT /evidence="ECO:0000269|PubMed:6244261"
FT MOD_RES 95
FT /note="N6,N6,N6-trimethyllysine"
FT /evidence="ECO:0000269|PubMed:6244261"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:1CCR"
FT HELIX 12..22
FT /evidence="ECO:0007829|PDB:1CCR"
FT TURN 23..26
FT /evidence="ECO:0007829|PDB:1CCR"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:1CCR"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:1CCR"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:1CCR"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:1CCR"
FT HELIX 97..110
FT /evidence="ECO:0007829|PDB:1CCR"
SQ SEQUENCE 112 AA; 12271 MW; C17D2B4628C77146 CRC64;
MASFSEAPPG NPKAGEKIFK TKCAQCHTVD KGAGHKQGPN LNGLFGRQSG TTPGYSYSTA
NKNMAVIWEE NTLYDYLLNP KKYIPGTKMV FPGLKKPQER ADLISYLKEA TS
