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Q0DI31

- CYC_ORYSJ

UniProt

Q0DI31 - CYC_ORYSJ

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Protein

Cytochrome c

Gene
CC-1, Os05g0420600, LOC_Os05g34770, OsJ_017825, OSJNBb0092E21.3, P0426G01.18
Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei23 – 231Heme (covalent)
Binding sitei26 – 261Heme (covalent)
Metal bindingi27 – 271Iron (heme axial ligand)
Metal bindingi89 – 891Iron (heme axial ligand)

GO - Molecular functioni

  1. copper ion binding Source: EnsemblPlants/Gramene
  2. electron carrier activity Source: InterPro
  3. heme binding Source: InterPro
  4. iron ion binding Source: InterPro

GO - Biological processi

  1. oxidation-reduction process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Electron transport, Respiratory chain, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

ReactomeiREACT_175687. Detoxification of Reactive Oxygen Species.
REACT_176102. Release of apoptotic factors from the mitochondria.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytochrome c
Gene namesi
Name:CC-1
Ordered Locus Names:Os05g0420600, LOC_Os05g34770
ORF Names:OsJ_017825, OSJNBb0092E21.3, P0426G01.18
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763: Chromosome 5

Organism-specific databases

GrameneiQ0DI31.

Subcellular locationi

Mitochondrion intermembrane space
Note: Loosely associated with the inner membrane.

GO - Cellular componenti

  1. cytosol Source: EnsemblPlants/Gramene
  2. mitochondrial intermembrane space Source: UniProtKB-SubCell
  3. respiratory chain Source: UniProtKB-KW
  4. vacuolar membrane Source: EnsemblPlants/Gramene
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 112111Cytochrome cPRO_0000108303Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine
Modified residuei81 – 811N6,N6,N6-trimethyllysine
Modified residuei95 – 951N6,N6,N6-trimethyllysine

Post-translational modificationi

Binds 1 heme group per subunit.

Keywords - PTMi

Acetylation, Methylation

Structurei

Secondary structure

1
112
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63
Helixi12 – 2211
Turni23 – 264
Beta strandi36 – 383
Helixi59 – 646
Helixi70 – 789
Helixi80 – 834
Helixi97 – 11014

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CCRX-ray1.50A2-112[»]
ProteinModelPortaliQ0DI31.
SMRiQ0DI31. Positions 2-112.

Miscellaneous databases

EvolutionaryTraceiQ0DI31.

Family & Domainsi

Sequence similaritiesi

Belongs to the cytochrome c family.

Phylogenomic databases

eggNOGiCOG3474.
KOiK08738.
OMAiWILADVE.

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
IPR002327. Cyt_c_1A/1B.
IPR003088. Cyt_c_dom.
[Graphical view]
PANTHERiPTHR11961. PTHR11961. 1 hit.
PfamiPF00034. Cytochrom_C. 1 hit.
[Graphical view]
PRINTSiPR00604. CYTCHRMECIAB.
SUPFAMiSSF46626. SSF46626. 1 hit.
PROSITEiPS51007. CYTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q0DI31-1 [UniParc]FASTAAdd to Basket

« Hide

MASFSEAPPG NPKAGEKIFK TKCAQCHTVD KGAGHKQGPN LNGLFGRQSG    50
TTPGYSYSTA NKNMAVIWEE NTLYDYLLNP KKYIPGTKMV FPGLKKPQER 100
ADLISYLKEA TS 112
Length:112
Mass (Da):12,271
Last modified:October 17, 2006 - v1
Checksum:iC17D2B4628C77146
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D12634 mRNA. Translation: BAA02159.1.
AC124836 Genomic DNA. Translation: AAT44244.1.
AC137623 Genomic DNA. Translation: AAV25652.1.
AP008211 Genomic DNA. Translation: BAF17492.1.
CM000142 Genomic DNA. Translation: EAZ34342.1.
PIRiJS0709. CCRZ.
RefSeqiNP_001055578.1. NM_001062113.1.
UniGeneiOs.57469.

Genome annotation databases

EnsemblPlantsiOS05T0420600-01; OS05T0420600-01; OS05G0420600.
GeneIDi4338825.
KEGGiosa:4338825.

Cross-referencesi

Web resourcesi

Protein Spotlight

Life shuttle - Issue 76 of November 2006

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D12634 mRNA. Translation: BAA02159.1 .
AC124836 Genomic DNA. Translation: AAT44244.1 .
AC137623 Genomic DNA. Translation: AAV25652.1 .
AP008211 Genomic DNA. Translation: BAF17492.1 .
CM000142 Genomic DNA. Translation: EAZ34342.1 .
PIRi JS0709. CCRZ.
RefSeqi NP_001055578.1. NM_001062113.1.
UniGenei Os.57469.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CCR X-ray 1.50 A 2-112 [» ]
ProteinModelPortali Q0DI31.
SMRi Q0DI31. Positions 2-112.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi OS05T0420600-01 ; OS05T0420600-01 ; OS05G0420600 .
GeneIDi 4338825.
KEGGi osa:4338825.

Organism-specific databases

Gramenei Q0DI31.

Phylogenomic databases

eggNOGi COG3474.
KOi K08738.
OMAi WILADVE.

Enzyme and pathway databases

Reactomei REACT_175687. Detoxification of Reactive Oxygen Species.
REACT_176102. Release of apoptotic factors from the mitochondria.

Miscellaneous databases

EvolutionaryTracei Q0DI31.

Family and domain databases

Gene3Di 1.10.760.10. 1 hit.
InterProi IPR009056. Cyt_c-like_dom.
IPR002327. Cyt_c_1A/1B.
IPR003088. Cyt_c_dom.
[Graphical view ]
PANTHERi PTHR11961. PTHR11961. 1 hit.
Pfami PF00034. Cytochrom_C. 1 hit.
[Graphical view ]
PRINTSi PR00604. CYTCHRMECIAB.
SUPFAMi SSF46626. SSF46626. 1 hit.
PROSITEi PS51007. CYTC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "cDNA cloning and sequence analysis of rice cytochrome c gene."
    Nishi R., Uchimiya H., Kato A.
    Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Yamahoushi.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  4. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  5. "The genomes of Oryza sativa: a history of duplications."
    Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
    , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
    PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  6. "Amino acid sequence of cytochrome c from rice."
    Mori E., Morita Y.
    J. Biochem. 87:249-266(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-112.
  7. "Structure of rice ferricytochrome c at 2.0-A resolution."
    Ochi H., Hata Y., Tanaka N., Kakudo M., Sakurai T., Aihara S., Morita Y.
    J. Mol. Biol. 166:407-418(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Entry informationi

Entry nameiCYC_ORYSJ
AccessioniPrimary (citable) accession number: Q0DI31
Secondary accession number(s): P00055, Q6L4Z1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: October 17, 2006
Last modified: September 3, 2014
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  3. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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