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Protein

Probable C->U-editing enzyme APOBEC-2

Gene

APOBEC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable C to U editing enzyme whose physiological substrate is not yet known. Does not display detectable apoB mRNA editing. Has a low intrinsic cytidine deaminase activity. May play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.1 Publication

Cofactori

Zn2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi60 – 601Zinc; catalytic
Metal bindingi98 – 981Zinc; catalytic
Active sitei100 – 1001Proton donor1 Publication
Metal bindingi128 – 1281Zinc; catalytic
Metal bindingi131 – 1311Zinc; catalytic

GO - Molecular functioni

  1. cytidine deaminase activity Source: ProtInc
  2. RNA binding Source: ProtInc
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. cytidine deamination Source: GOC
  2. DNA demethylation Source: UniProtKB
  3. mRNA modification Source: Ensembl
  4. mRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Probable C->U-editing enzyme APOBEC-2 (EC:3.5.4.-)
Gene namesi
Name:APOBEC2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:605. APOBEC2.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA24890.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 224224Probable C->U-editing enzyme APOBEC-2PRO_0000171749Add
BLAST

Proteomic databases

PaxDbiQ9Y235.
PRIDEiQ9Y235.

PTM databases

PhosphoSiteiQ9Y235.

Expressioni

Tissue specificityi

Expressed exclusively in heart and skeletal muscle.

Gene expression databases

BgeeiQ9Y235.
CleanExiHS_APOBEC2.
GenevestigatoriQ9Y235.

Organism-specific databases

HPAiHPA014252.
HPA017957.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi116133. 1 interaction.
DIPiDIP-60263N.
STRINGi9606.ENSP00000244669.

Structurei

Secondary structure

1
224
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi48 – 536Combined sources
Turni54 – 563Combined sources
Beta strandi62 – 643Combined sources
Beta strandi68 – 7710Combined sources
Beta strandi83 – 9412Combined sources
Helixi99 – 1068Combined sources
Beta strandi116 – 12510Combined sources
Helixi129 – 14113Combined sources
Beta strandi145 – 1539Combined sources
Helixi160 – 17112Combined sources
Beta strandi175 – 1784Combined sources
Helixi181 – 19111Combined sources
Helixi208 – 22316Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NYTX-ray2.50A/B/C/D41-224[»]
ProteinModelPortaliQ9Y235.
SMRiQ9Y235. Positions 41-224.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y235.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini64 – 169106CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG44965.
GeneTreeiENSGT00530000062933.
HOGENOMiHOG000033754.
HOVERGENiHBG107155.
KOiK18772.
OMAiCRLRIMK.
OrthoDBiEOG7VHSZC.
PhylomeDBiQ9Y235.
TreeFamiTF331356.

Family and domain databases

InterProiIPR007904. APOBEC_C.
IPR013158. APOBEC_N.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF05240. APOBEC_C. 1 hit.
PF08210. APOBEC_N. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
PROSITEiPS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Y235-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQKEEAAVA TEAASQNGED LENLDDPEKL KELIELPPFE IVTGERLPAN
60 70 80 90 100
FFKFQFRNVE YSSGRNKTFL CYVVEAQGKG GQVQASRGYL EDEHAAAHAE
110 120 130 140 150
EAFFNTILPA FDPALRYNVT WYVSSSPCAA CADRIIKTLS KTKNLRLLIL
160 170 180 190 200
VGRLFMWEEP EIQAALKKLK EAGCKLRIMK PQDFEYVWQN FVEQEEGESK
210 220
AFQPWEDIQE NFLYYEEKLA DILK
Length:224
Mass (Da):25,703
Last modified:November 1, 1999 - v1
Checksum:iCA0905AFAA8C8FA1
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti136 – 1361I → T.1 Publication
Corresponds to variant rs2076472 [ dbSNP | Ensembl ].
VAR_024406

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF161698 mRNA. Translation: AAD45360.1.
AK223461 mRNA. Translation: BAD97181.1.
AK313288 mRNA. Translation: BAG36096.1.
AL031778 Genomic DNA. Translation: CAB44740.1.
CH471081 Genomic DNA. Translation: EAX04009.1.
BC047767 mRNA. Translation: AAH47767.1.
BC069688 mRNA. Translation: AAH69688.1.
BC069764 mRNA. Translation: AAH69764.1.
CCDSiCCDS4848.1.
RefSeqiNP_006780.1. NM_006789.3.
UniGeneiHs.555915.

Genome annotation databases

EnsembliENST00000244669; ENSP00000244669; ENSG00000124701.
GeneIDi10930.
KEGGihsa:10930.
UCSCiuc003opl.3. human.

Polymorphism databases

DMDMi23396446.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF161698 mRNA. Translation: AAD45360.1.
AK223461 mRNA. Translation: BAD97181.1.
AK313288 mRNA. Translation: BAG36096.1.
AL031778 Genomic DNA. Translation: CAB44740.1.
CH471081 Genomic DNA. Translation: EAX04009.1.
BC047767 mRNA. Translation: AAH47767.1.
BC069688 mRNA. Translation: AAH69688.1.
BC069764 mRNA. Translation: AAH69764.1.
CCDSiCCDS4848.1.
RefSeqiNP_006780.1. NM_006789.3.
UniGeneiHs.555915.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NYTX-ray2.50A/B/C/D41-224[»]
ProteinModelPortaliQ9Y235.
SMRiQ9Y235. Positions 41-224.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116133. 1 interaction.
DIPiDIP-60263N.
STRINGi9606.ENSP00000244669.

PTM databases

PhosphoSiteiQ9Y235.

Polymorphism databases

DMDMi23396446.

Proteomic databases

PaxDbiQ9Y235.
PRIDEiQ9Y235.

Protocols and materials databases

DNASUi10930.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000244669; ENSP00000244669; ENSG00000124701.
GeneIDi10930.
KEGGihsa:10930.
UCSCiuc003opl.3. human.

Organism-specific databases

CTDi10930.
GeneCardsiGC06P041020.
HGNCiHGNC:605. APOBEC2.
HPAiHPA014252.
HPA017957.
MIMi604797. gene.
neXtProtiNX_Q9Y235.
PharmGKBiPA24890.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG44965.
GeneTreeiENSGT00530000062933.
HOGENOMiHOG000033754.
HOVERGENiHBG107155.
KOiK18772.
OMAiCRLRIMK.
OrthoDBiEOG7VHSZC.
PhylomeDBiQ9Y235.
TreeFamiTF331356.

Miscellaneous databases

EvolutionaryTraceiQ9Y235.
GeneWikiiAPOBEC2.
GenomeRNAii10930.
NextBioi41523.
PROiQ9Y235.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y235.
CleanExiHS_APOBEC2.
GenevestigatoriQ9Y235.

Family and domain databases

InterProiIPR007904. APOBEC_C.
IPR013158. APOBEC_N.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF05240. APOBEC_C. 1 hit.
PF08210. APOBEC_N. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
PROSITEiPS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "APOBEC-2, a cardiac- and skeletal muscle-specific member of the cytidine deaminase supergene family."
    Liao W., Hong S.-H., Chan B.H.-J., Rudolph F.B., Clark S.C., Chan L.
    Biochem. Biophys. Res. Commun. 260:398-404(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Heart.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Skeletal muscle.
  3. Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT THR-136.
    Tissue: Pancreas.
  4. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: PNS.
  7. "Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain."
    Guo J.U., Su Y., Zhong C., Ming G.L., Song H.
    Cell 145:423-434(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DNA DEMETHYLATION.
  8. "The APOBEC-2 crystal structure and functional implications for the deaminase AID."
    Prochnow C., Bransteitter R., Klein M.G., Goodman M.F., Chen X.S.
    Nature 445:447-451(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 41-224, SUBUNIT, COFACTOR, ACTIVE SITE, ZINC-BINDING SITES.

Entry informationi

Entry nameiABEC2_HUMAN
AccessioniPrimary (citable) accession number: Q9Y235
Secondary accession number(s): B2R899
, Q53F28, Q5TGU5, Q5TGU6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: November 1, 1999
Last modified: April 1, 2015
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.