Full text data of APOBEC2
APOBEC2
[Confidence: low (only semi-automatic identification from reviews)]
Probable C->U-editing enzyme APOBEC-2; 3.5.4.-
Note: presumably soluble (membrane word is not in UniProt keywords or features)
Probable C->U-editing enzyme APOBEC-2; 3.5.4.-
Note: presumably soluble (membrane word is not in UniProt keywords or features)
UniProt
Q9Y235
ID ABEC2_HUMAN Reviewed; 224 AA.
AC Q9Y235; B2R899; Q53F28; Q5TGU5; Q5TGU6;
DT 19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
read moreDT 01-NOV-1999, sequence version 1.
DT 22-JAN-2014, entry version 102.
DE RecName: Full=Probable C->U-editing enzyme APOBEC-2;
DE EC=3.5.4.-;
GN Name=APOBEC2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Heart;
RX PubMed=10403781; DOI=10.1006/bbrc.1999.0925;
RA Liao W., Hong S.-H., Chan B.H.-J., Rudolph F.B., Clark S.C., Chan L.;
RT "APOBEC-2, a cardiac- and skeletal muscle-specific member of the
RT cytidine deaminase supergene family.";
RL Biochem. Biophys. Res. Commun. 260:398-404(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Skeletal muscle;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT THR-136.
RC TISSUE=Pancreas;
RA Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=14574404; DOI=10.1038/nature02055;
RA Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L.,
RA Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E.,
RA Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Andrews T.D., Ashwell R.I.S.,
RA Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J.,
RA Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P.,
RA Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Carder C., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V.,
RA Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J.,
RA Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E.,
RA Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A.,
RA Frankland J., French L., Garner P., Garnett J., Ghori M.J.,
RA Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M.,
RA Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S.,
RA Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R.,
RA Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E.,
RA Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A.,
RA Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C.,
RA Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M.,
RA Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M.,
RA Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K.,
RA McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T.,
RA Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R.,
RA Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W.,
RA Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M.,
RA Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L.,
RA Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J.,
RA Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B.,
RA Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L.,
RA Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W.,
RA Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A.,
RA Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.;
RT "The DNA sequence and analysis of human chromosome 6.";
RL Nature 425:805-811(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=PNS;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [7]
RP FUNCTION IN DNA DEMETHYLATION.
RX PubMed=21496894; DOI=10.1016/j.cell.2011.03.022;
RA Guo J.U., Su Y., Zhong C., Ming G.L., Song H.;
RT "Hydroxylation of 5-methylcytosine by TET1 promotes active DNA
RT demethylation in the adult brain.";
RL Cell 145:423-434(2011).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 41-224, SUBUNIT, COFACTOR,
RP ACTIVE SITE, AND ZINC-BINDING SITES.
RX PubMed=17187054; DOI=10.1038/nature05492;
RA Prochnow C., Bransteitter R., Klein M.G., Goodman M.F., Chen X.S.;
RT "The APOBEC-2 crystal structure and functional implications for the
RT deaminase AID.";
RL Nature 445:447-451(2007).
CC -!- FUNCTION: Probable C to U editing enzyme whose physiological
CC substrate is not yet known. Does not display detectable apoB mRNA
CC editing. Has a low intrinsic cytidine deaminase activity. May play
CC a role in the epigenetic regulation of gene expression through the
CC process of active DNA demethylation.
CC -!- COFACTOR: Zinc (By similarity).
CC -!- SUBUNIT: Homotetramer.
CC -!- TISSUE SPECIFICITY: Expressed exclusively in heart and skeletal
CC muscle.
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family.
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DR EMBL; AF161698; AAD45360.1; -; mRNA.
DR EMBL; AK223461; BAD97181.1; -; mRNA.
DR EMBL; AK313288; BAG36096.1; -; mRNA.
DR EMBL; AL031778; CAB44740.1; -; Genomic_DNA.
DR EMBL; CH471081; EAX04009.1; -; Genomic_DNA.
DR EMBL; BC047767; AAH47767.1; -; mRNA.
DR EMBL; BC069688; AAH69688.1; -; mRNA.
DR EMBL; BC069764; AAH69764.1; -; mRNA.
DR RefSeq; NP_006780.1; NM_006789.3.
DR UniGene; Hs.555915; -.
DR PDB; 2NYT; X-ray; 2.50 A; A/B/C/D=41-224.
DR PDBsum; 2NYT; -.
DR ProteinModelPortal; Q9Y235; -.
DR SMR; Q9Y235; 41-224.
DR DIP; DIP-60263N; -.
DR STRING; 9606.ENSP00000244669; -.
DR PhosphoSite; Q9Y235; -.
DR DMDM; 23396446; -.
DR PaxDb; Q9Y235; -.
DR PRIDE; Q9Y235; -.
DR DNASU; 10930; -.
DR Ensembl; ENST00000244669; ENSP00000244669; ENSG00000124701.
DR GeneID; 10930; -.
DR KEGG; hsa:10930; -.
DR UCSC; uc003opl.3; human.
DR CTD; 10930; -.
DR GeneCards; GC06P041020; -.
DR HGNC; HGNC:605; APOBEC2.
DR HPA; HPA014252; -.
DR HPA; HPA017957; -.
DR MIM; 604797; gene.
DR neXtProt; NX_Q9Y235; -.
DR PharmGKB; PA24890; -.
DR eggNOG; NOG44965; -.
DR HOGENOM; HOG000033754; -.
DR HOVERGEN; HBG107155; -.
DR InParanoid; Q9Y235; -.
DR KO; K01500; -.
DR OMA; CRLRIMK; -.
DR OrthoDB; EOG7VHSZC; -.
DR PhylomeDB; Q9Y235; -.
DR EvolutionaryTrace; Q9Y235; -.
DR GeneWiki; APOBEC2; -.
DR GenomeRNAi; 10930; -.
DR NextBio; 41523; -.
DR PRO; PR:Q9Y235; -.
DR Bgee; Q9Y235; -.
DR CleanEx; HS_APOBEC2; -.
DR Genevestigator; Q9Y235; -.
DR GO; GO:0004126; F:cytidine deaminase activity; TAS:ProtInc.
DR GO; GO:0003723; F:RNA binding; TAS:ProtInc.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IDA:UniProtKB.
DR GO; GO:0016556; P:mRNA modification; IEA:Ensembl.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR InterPro; IPR007904; APOBEC_C.
DR InterPro; IPR013158; APOBEC_N.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR Pfam; PF05240; APOBEC_C; 1.
DR Pfam; PF08210; APOBEC_N; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES; FALSE_NEG.
PE 1: Evidence at protein level;
KW 3D-structure; Complete proteome; Hydrolase; Metal-binding;
KW mRNA processing; Polymorphism; Reference proteome; Zinc.
FT CHAIN 1 224 Probable C->U-editing enzyme APOBEC-2.
FT /FTId=PRO_0000171749.
FT ACT_SITE 100 100 Proton donor.
FT METAL 60 60 Zinc; catalytic.
FT METAL 98 98 Zinc; catalytic.
FT METAL 128 128 Zinc; catalytic.
FT METAL 131 131 Zinc; catalytic.
FT VARIANT 136 136 I -> T (in dbSNP:rs2076472).
FT /FTId=VAR_024406.
FT HELIX 48 53
FT TURN 54 56
FT STRAND 62 64
FT STRAND 68 77
FT STRAND 83 94
FT HELIX 99 106
FT STRAND 116 125
FT HELIX 129 141
FT STRAND 145 153
FT HELIX 160 171
FT STRAND 175 178
FT HELIX 181 191
FT HELIX 208 223
SQ SEQUENCE 224 AA; 25703 MW; CA0905AFAA8C8FA1 CRC64;
MAQKEEAAVA TEAASQNGED LENLDDPEKL KELIELPPFE IVTGERLPAN FFKFQFRNVE
YSSGRNKTFL CYVVEAQGKG GQVQASRGYL EDEHAAAHAE EAFFNTILPA FDPALRYNVT
WYVSSSPCAA CADRIIKTLS KTKNLRLLIL VGRLFMWEEP EIQAALKKLK EAGCKLRIMK
PQDFEYVWQN FVEQEEGESK AFQPWEDIQE NFLYYEEKLA DILK
//
ID ABEC2_HUMAN Reviewed; 224 AA.
AC Q9Y235; B2R899; Q53F28; Q5TGU5; Q5TGU6;
DT 19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
read moreDT 01-NOV-1999, sequence version 1.
DT 22-JAN-2014, entry version 102.
DE RecName: Full=Probable C->U-editing enzyme APOBEC-2;
DE EC=3.5.4.-;
GN Name=APOBEC2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Heart;
RX PubMed=10403781; DOI=10.1006/bbrc.1999.0925;
RA Liao W., Hong S.-H., Chan B.H.-J., Rudolph F.B., Clark S.C., Chan L.;
RT "APOBEC-2, a cardiac- and skeletal muscle-specific member of the
RT cytidine deaminase supergene family.";
RL Biochem. Biophys. Res. Commun. 260:398-404(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Skeletal muscle;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT THR-136.
RC TISSUE=Pancreas;
RA Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=14574404; DOI=10.1038/nature02055;
RA Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L.,
RA Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E.,
RA Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Andrews T.D., Ashwell R.I.S.,
RA Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J.,
RA Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P.,
RA Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Carder C., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V.,
RA Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J.,
RA Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E.,
RA Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A.,
RA Frankland J., French L., Garner P., Garnett J., Ghori M.J.,
RA Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M.,
RA Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S.,
RA Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R.,
RA Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E.,
RA Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A.,
RA Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C.,
RA Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M.,
RA Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M.,
RA Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K.,
RA McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T.,
RA Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R.,
RA Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W.,
RA Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M.,
RA Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L.,
RA Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J.,
RA Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B.,
RA Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L.,
RA Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W.,
RA Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A.,
RA Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.;
RT "The DNA sequence and analysis of human chromosome 6.";
RL Nature 425:805-811(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=PNS;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [7]
RP FUNCTION IN DNA DEMETHYLATION.
RX PubMed=21496894; DOI=10.1016/j.cell.2011.03.022;
RA Guo J.U., Su Y., Zhong C., Ming G.L., Song H.;
RT "Hydroxylation of 5-methylcytosine by TET1 promotes active DNA
RT demethylation in the adult brain.";
RL Cell 145:423-434(2011).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 41-224, SUBUNIT, COFACTOR,
RP ACTIVE SITE, AND ZINC-BINDING SITES.
RX PubMed=17187054; DOI=10.1038/nature05492;
RA Prochnow C., Bransteitter R., Klein M.G., Goodman M.F., Chen X.S.;
RT "The APOBEC-2 crystal structure and functional implications for the
RT deaminase AID.";
RL Nature 445:447-451(2007).
CC -!- FUNCTION: Probable C to U editing enzyme whose physiological
CC substrate is not yet known. Does not display detectable apoB mRNA
CC editing. Has a low intrinsic cytidine deaminase activity. May play
CC a role in the epigenetic regulation of gene expression through the
CC process of active DNA demethylation.
CC -!- COFACTOR: Zinc (By similarity).
CC -!- SUBUNIT: Homotetramer.
CC -!- TISSUE SPECIFICITY: Expressed exclusively in heart and skeletal
CC muscle.
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family.
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DR EMBL; AF161698; AAD45360.1; -; mRNA.
DR EMBL; AK223461; BAD97181.1; -; mRNA.
DR EMBL; AK313288; BAG36096.1; -; mRNA.
DR EMBL; AL031778; CAB44740.1; -; Genomic_DNA.
DR EMBL; CH471081; EAX04009.1; -; Genomic_DNA.
DR EMBL; BC047767; AAH47767.1; -; mRNA.
DR EMBL; BC069688; AAH69688.1; -; mRNA.
DR EMBL; BC069764; AAH69764.1; -; mRNA.
DR RefSeq; NP_006780.1; NM_006789.3.
DR UniGene; Hs.555915; -.
DR PDB; 2NYT; X-ray; 2.50 A; A/B/C/D=41-224.
DR PDBsum; 2NYT; -.
DR ProteinModelPortal; Q9Y235; -.
DR SMR; Q9Y235; 41-224.
DR DIP; DIP-60263N; -.
DR STRING; 9606.ENSP00000244669; -.
DR PhosphoSite; Q9Y235; -.
DR DMDM; 23396446; -.
DR PaxDb; Q9Y235; -.
DR PRIDE; Q9Y235; -.
DR DNASU; 10930; -.
DR Ensembl; ENST00000244669; ENSP00000244669; ENSG00000124701.
DR GeneID; 10930; -.
DR KEGG; hsa:10930; -.
DR UCSC; uc003opl.3; human.
DR CTD; 10930; -.
DR GeneCards; GC06P041020; -.
DR HGNC; HGNC:605; APOBEC2.
DR HPA; HPA014252; -.
DR HPA; HPA017957; -.
DR MIM; 604797; gene.
DR neXtProt; NX_Q9Y235; -.
DR PharmGKB; PA24890; -.
DR eggNOG; NOG44965; -.
DR HOGENOM; HOG000033754; -.
DR HOVERGEN; HBG107155; -.
DR InParanoid; Q9Y235; -.
DR KO; K01500; -.
DR OMA; CRLRIMK; -.
DR OrthoDB; EOG7VHSZC; -.
DR PhylomeDB; Q9Y235; -.
DR EvolutionaryTrace; Q9Y235; -.
DR GeneWiki; APOBEC2; -.
DR GenomeRNAi; 10930; -.
DR NextBio; 41523; -.
DR PRO; PR:Q9Y235; -.
DR Bgee; Q9Y235; -.
DR CleanEx; HS_APOBEC2; -.
DR Genevestigator; Q9Y235; -.
DR GO; GO:0004126; F:cytidine deaminase activity; TAS:ProtInc.
DR GO; GO:0003723; F:RNA binding; TAS:ProtInc.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IDA:UniProtKB.
DR GO; GO:0016556; P:mRNA modification; IEA:Ensembl.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR InterPro; IPR007904; APOBEC_C.
DR InterPro; IPR013158; APOBEC_N.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR Pfam; PF05240; APOBEC_C; 1.
DR Pfam; PF08210; APOBEC_N; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES; FALSE_NEG.
PE 1: Evidence at protein level;
KW 3D-structure; Complete proteome; Hydrolase; Metal-binding;
KW mRNA processing; Polymorphism; Reference proteome; Zinc.
FT CHAIN 1 224 Probable C->U-editing enzyme APOBEC-2.
FT /FTId=PRO_0000171749.
FT ACT_SITE 100 100 Proton donor.
FT METAL 60 60 Zinc; catalytic.
FT METAL 98 98 Zinc; catalytic.
FT METAL 128 128 Zinc; catalytic.
FT METAL 131 131 Zinc; catalytic.
FT VARIANT 136 136 I -> T (in dbSNP:rs2076472).
FT /FTId=VAR_024406.
FT HELIX 48 53
FT TURN 54 56
FT STRAND 62 64
FT STRAND 68 77
FT STRAND 83 94
FT HELIX 99 106
FT STRAND 116 125
FT HELIX 129 141
FT STRAND 145 153
FT HELIX 160 171
FT STRAND 175 178
FT HELIX 181 191
FT HELIX 208 223
SQ SEQUENCE 224 AA; 25703 MW; CA0905AFAA8C8FA1 CRC64;
MAQKEEAAVA TEAASQNGED LENLDDPEKL KELIELPPFE IVTGERLPAN FFKFQFRNVE
YSSGRNKTFL CYVVEAQGKG GQVQASRGYL EDEHAAAHAE EAFFNTILPA FDPALRYNVT
WYVSSSPCAA CADRIIKTLS KTKNLRLLIL VGRLFMWEEP EIQAALKKLK EAGCKLRIMK
PQDFEYVWQN FVEQEEGESK AFQPWEDIQE NFLYYEEKLA DILK
//
MIM
604797
*RECORD*
*FIELD* NO
604797
*FIELD* TI
*604797 APOLIPOPROTEIN B mRNA-EDITING ENZYME, CATALYTIC POLYPEPTIDE-LIKE 2;
APOBEC2
read more;;APOBEC1-LIKE
*FIELD* TX
CLONING
APOBEC1 (600130) is a member of the cytidine deaminase superfamily. By
searching an EST database using the mouse Apobec1 amino acid sequence as
the query, Liao et al. (1999) identified several human and mouse ESTs
encoding polypeptides with sequence similarity to Apobec1, mainly in the
region of the cytidine deaminase domain. Using 1 of the mouse ESTs to
screen a human heart cDNA library, they isolated a cDNA encoding a
protein that they named APOBEC2. The deduced APOBEC2 protein has 224
amino acids. Phylogenetic analysis of the cytidine deaminase superfamily
based on the catalytic domains of the proteins indicated that APOBEC2 is
evolutionarily closer to APOBEC1 than to the other members. Compared
with APOBEC1, APOBEC2 has a longer N-terminal region and a shorter
C-terminal region. Northern blot analysis showed that APOBEC2 was
expressed exclusively in heart and skeletal muscle. APOBEC2 expression
was not detected in brain, lung, liver, pancreas, small intestine,
colon, kidney, spleen, thymus, leukocyte, testis, uterus, placenta, or
prostate.
By Northern, Western, and immunohistochemical analyses of mouse muscle,
Sato et al. (2010) found that Apobec2 was expressed predominantly in
slow muscle fibers. Apobec2 expression increased during late
differentiation in neonatal mouse myoblasts and the C2C12 mouse myoblast
cell line. Gel filtration of mouse gastrocnemius muscle revealed that
Apobec2 formed a soluble tetramer.
GENE FUNCTION
Liao et al. (1999) found that recombinant APOBEC2 had low, but definite,
intrinsic cytidine deaminase activity in an in vitro assay. However,
unlike APOBEC1, APOBEC2 did not recognize APOB (107730) mRNA as a
substrate.
Sato et al. (2010) showed that Apobec2 expression increased with
denervation of mouse soleus and extensor digitorum longus muscle, which
was accompanied by an increase in the proportion of slow muscle fibers.
Unlike APOBEC1, Apobec2 did not bind RNA, which is a critical
characteristic of RNA-editing enzymes.
BIOCHEMICAL FEATURES
- Crystal Structure
Prochnow et al. (2007) reported the crystal structure of APOBEC2.
APOBEC2 forms a rod-shaped tetramer that differs markedly from the
square-shaped tetramer of the free nucleotide cytidine deaminase (AID;
605257), with which APOBEC proteins share considerable sequence
homology. In APOBEC2, 2 long alpha-helices of a monomer structure
prevent the formation of a square-shaped tetramer and facilitate
formation of the rod-shaped tetramer via head-to-head interaction of 2
APOBEC2 dimers. Extensive sequence homology among APOBEC family members
allowed Prochnow et al. (2007) to test APOBEC2 structure-based
predictions using AID. Prochnow et al. (2007) showed that AID
deamination activity is impaired by mutations predicted to interfere
with oligomerization and substrate access. The structure suggested how
mutations in patients with hyper-IgM-2 syndrome (605258) inactivate AID,
resulting in defective antibody maturation.
MAPPING
By radiation hybrid mapping, Liao et al. (1999) mapped the human APOBEC2
gene to chromosome 6. Liao et al. (1999) mapped the mouse Apobec2 gene
to chromosome 17, where it is located distal to D17Bir7 and proximal to
D17Mit85. Based on the homology of synteny between this region of mouse
chromosome 17 and human 6p21, Liao et al. (1999) concluded that the
human APOBEC2 gene localizes to 6p21.
ANIMAL MODEL
Sato et al. (2010) found that Apobec2 -/- mice were viable, appeared
normal, and were fertile. However, they were smaller than wildtype mice
at birth and throughout life. Apobec2 -/- mice developed a mild myopathy
with age, which was accompanied by an increase in the proportion of slow
muscle fibers.
*FIELD* RF
1. Liao, W.; Hong, S.-H.; Chan, B. H.-J.; Rudolph, F. B.; Clark, S.
C.; Chan, L.: APOBEC-2, a cardiac- and skeletal muscle-specific member
of the cytidine deaminase supergene family. Biochem. Biophys. Res.
Commun. 260: 398-404, 1999.
2. Prochnow, C.; Bransteitter, R.; Klein, M. G.; Goodman, M. F.; Chen,
X. S.: The APOBEC-2 crystal structure and functional implications
for the deaminase AID. Nature 445: 447-451, 2007.
3. Sato, Y.; Probst, H. C.; Tatsumi, R.; Ikeuchi, Y.; Neuberger, M.
S.; Rada, C.: Deficiency in APOBEC2 leads to a shift in muscle fiber
type, diminished body mass, and myopathy. J. Biol. Chem. 285: 7111-7118,
2010.
*FIELD* CN
Patricia A. Hartz - updated: 11/30/2011
Ada Hamosh - updated: 2/23/2007
*FIELD* CD
Patti M. Sherman: 4/5/2000
*FIELD* ED
mgross: 02/07/2012
terry: 11/30/2011
alopez: 3/2/2007
terry: 2/23/2007
alopez: 2/7/2005
mgross: 5/5/2003
mgross: 8/23/2002
psherman: 5/3/2000
alopez: 5/3/2000
mcapotos: 4/18/2000
psherman: 4/6/2000
*RECORD*
*FIELD* NO
604797
*FIELD* TI
*604797 APOLIPOPROTEIN B mRNA-EDITING ENZYME, CATALYTIC POLYPEPTIDE-LIKE 2;
APOBEC2
read more;;APOBEC1-LIKE
*FIELD* TX
CLONING
APOBEC1 (600130) is a member of the cytidine deaminase superfamily. By
searching an EST database using the mouse Apobec1 amino acid sequence as
the query, Liao et al. (1999) identified several human and mouse ESTs
encoding polypeptides with sequence similarity to Apobec1, mainly in the
region of the cytidine deaminase domain. Using 1 of the mouse ESTs to
screen a human heart cDNA library, they isolated a cDNA encoding a
protein that they named APOBEC2. The deduced APOBEC2 protein has 224
amino acids. Phylogenetic analysis of the cytidine deaminase superfamily
based on the catalytic domains of the proteins indicated that APOBEC2 is
evolutionarily closer to APOBEC1 than to the other members. Compared
with APOBEC1, APOBEC2 has a longer N-terminal region and a shorter
C-terminal region. Northern blot analysis showed that APOBEC2 was
expressed exclusively in heart and skeletal muscle. APOBEC2 expression
was not detected in brain, lung, liver, pancreas, small intestine,
colon, kidney, spleen, thymus, leukocyte, testis, uterus, placenta, or
prostate.
By Northern, Western, and immunohistochemical analyses of mouse muscle,
Sato et al. (2010) found that Apobec2 was expressed predominantly in
slow muscle fibers. Apobec2 expression increased during late
differentiation in neonatal mouse myoblasts and the C2C12 mouse myoblast
cell line. Gel filtration of mouse gastrocnemius muscle revealed that
Apobec2 formed a soluble tetramer.
GENE FUNCTION
Liao et al. (1999) found that recombinant APOBEC2 had low, but definite,
intrinsic cytidine deaminase activity in an in vitro assay. However,
unlike APOBEC1, APOBEC2 did not recognize APOB (107730) mRNA as a
substrate.
Sato et al. (2010) showed that Apobec2 expression increased with
denervation of mouse soleus and extensor digitorum longus muscle, which
was accompanied by an increase in the proportion of slow muscle fibers.
Unlike APOBEC1, Apobec2 did not bind RNA, which is a critical
characteristic of RNA-editing enzymes.
BIOCHEMICAL FEATURES
- Crystal Structure
Prochnow et al. (2007) reported the crystal structure of APOBEC2.
APOBEC2 forms a rod-shaped tetramer that differs markedly from the
square-shaped tetramer of the free nucleotide cytidine deaminase (AID;
605257), with which APOBEC proteins share considerable sequence
homology. In APOBEC2, 2 long alpha-helices of a monomer structure
prevent the formation of a square-shaped tetramer and facilitate
formation of the rod-shaped tetramer via head-to-head interaction of 2
APOBEC2 dimers. Extensive sequence homology among APOBEC family members
allowed Prochnow et al. (2007) to test APOBEC2 structure-based
predictions using AID. Prochnow et al. (2007) showed that AID
deamination activity is impaired by mutations predicted to interfere
with oligomerization and substrate access. The structure suggested how
mutations in patients with hyper-IgM-2 syndrome (605258) inactivate AID,
resulting in defective antibody maturation.
MAPPING
By radiation hybrid mapping, Liao et al. (1999) mapped the human APOBEC2
gene to chromosome 6. Liao et al. (1999) mapped the mouse Apobec2 gene
to chromosome 17, where it is located distal to D17Bir7 and proximal to
D17Mit85. Based on the homology of synteny between this region of mouse
chromosome 17 and human 6p21, Liao et al. (1999) concluded that the
human APOBEC2 gene localizes to 6p21.
ANIMAL MODEL
Sato et al. (2010) found that Apobec2 -/- mice were viable, appeared
normal, and were fertile. However, they were smaller than wildtype mice
at birth and throughout life. Apobec2 -/- mice developed a mild myopathy
with age, which was accompanied by an increase in the proportion of slow
muscle fibers.
*FIELD* RF
1. Liao, W.; Hong, S.-H.; Chan, B. H.-J.; Rudolph, F. B.; Clark, S.
C.; Chan, L.: APOBEC-2, a cardiac- and skeletal muscle-specific member
of the cytidine deaminase supergene family. Biochem. Biophys. Res.
Commun. 260: 398-404, 1999.
2. Prochnow, C.; Bransteitter, R.; Klein, M. G.; Goodman, M. F.; Chen,
X. S.: The APOBEC-2 crystal structure and functional implications
for the deaminase AID. Nature 445: 447-451, 2007.
3. Sato, Y.; Probst, H. C.; Tatsumi, R.; Ikeuchi, Y.; Neuberger, M.
S.; Rada, C.: Deficiency in APOBEC2 leads to a shift in muscle fiber
type, diminished body mass, and myopathy. J. Biol. Chem. 285: 7111-7118,
2010.
*FIELD* CN
Patricia A. Hartz - updated: 11/30/2011
Ada Hamosh - updated: 2/23/2007
*FIELD* CD
Patti M. Sherman: 4/5/2000
*FIELD* ED
mgross: 02/07/2012
terry: 11/30/2011
alopez: 3/2/2007
terry: 2/23/2007
alopez: 2/7/2005
mgross: 5/5/2003
mgross: 8/23/2002
psherman: 5/3/2000
alopez: 5/3/2000
mcapotos: 4/18/2000
psherman: 4/6/2000