AKB9B_ARATH
ID AKB9B_ARATH Reviewed; 507 AA.
AC Q9SL49;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=RNA demethylase ALKBH9B {ECO:0000305};
DE Short=AtALKBH9B {ECO:0000303|PubMed:28923956};
DE EC=1.14.11.53 {ECO:0000269|PubMed:28923956};
DE AltName: Full=Alkylated DNA repair protein alkB homolog 9B {ECO:0000305};
DE AltName: Full=Alpha-ketoglutarate-dependent dioxygenase alkB homolog 9B {ECO:0000305};
GN Name=ALKBH9B {ECO:0000303|PubMed:28923956};
GN OrderedLocusNames=At2g17970 {ECO:0000312|Araport:AT2G17970};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, INTERACTION WITH THE COAT PROTEIN
RP OF ALFALFA MOSAIC VIRUS, AND SUBCELLULAR LOCATION.
RX PubMed=28923956; DOI=10.1073/pnas.1703139114;
RA Martinez-Perez M., Aparicio F., Lopez-Gresa M.P., Belles J.M.,
RA Sanchez-Navarro J.A., Pallas V.;
RT "Arabidopsis m6A demethylase activity modulates viral infection of a plant
RT virus and the m6A abundance in its genomic RNAs.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:10755-10760(2017).
CC -!- FUNCTION: Dioxygenase that demethylates RNA by oxidative demethylation:
CC specifically demethylates N(6)-methyladenosine (m6A) RNA, the most
CC prevalent internal modification of messenger RNA (mRNA) in higher
CC eukaryotes (PubMed:28923956). Modulates viral infection of the alfalfa
CC mosaic virus (AMV) and the m6A abundance in its genomic RNAs
CC (PubMed:28923956). {ECO:0000269|PubMed:28923956}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + an N(6)-methyladenosine in mRNA + O2 = an
CC adenosine in mRNA + CO2 + formaldehyde + succinate;
CC Xref=Rhea:RHEA:49520, Rhea:RHEA-COMP:12414, Rhea:RHEA-COMP:12417,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:74411,
CC ChEBI:CHEBI:74449; EC=1.14.11.53;
CC Evidence={ECO:0000269|PubMed:28923956};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00805};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00805};
CC -!- SUBUNIT: (Microbial infection) Interacts with the capsid protein ORF3b
CC of the alfalfa mosaic virus (AMV). {ECO:0000269|PubMed:28923956}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, P-body {ECO:0000269|PubMed:28923956}.
CC Cytoplasmic granule {ECO:0000269|PubMed:28923956}.
CC -!- SIMILARITY: Belongs to the alkB family. {ECO:0000305}.
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DR EMBL; AC006201; AAD20129.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06706.1; -; Genomic_DNA.
DR EMBL; BT010563; AAQ65186.1; -; mRNA.
DR EMBL; AK175991; BAD43754.1; -; mRNA.
DR PIR; F84558; F84558.
DR PIR; T00828; T00828.
DR RefSeq; NP_179387.1; NM_127351.3.
DR AlphaFoldDB; Q9SL49; -.
DR SMR; Q9SL49; -.
DR STRING; 3702.AT2G17970.1; -.
DR PaxDb; Q9SL49; -.
DR PRIDE; Q9SL49; -.
DR EnsemblPlants; AT2G17970.1; AT2G17970.1; AT2G17970.
DR GeneID; 816307; -.
DR Gramene; AT2G17970.1; AT2G17970.1; AT2G17970.
DR KEGG; ath:AT2G17970; -.
DR Araport; AT2G17970; -.
DR TAIR; locus:2060964; AT2G17970.
DR eggNOG; KOG4176; Eukaryota.
DR InParanoid; Q9SL49; -.
DR OrthoDB; 722070at2759; -.
DR PhylomeDB; Q9SL49; -.
DR PRO; PR:Q9SL49; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SL49; baseline and differential.
DR GO; GO:0000932; C:P-body; IDA:UniProtKB.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0032451; F:demethylase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:1990931; F:mRNA N6-methyladenosine dioxygenase activity; IEA:RHEA.
DR GO; GO:0070988; P:demethylation; IDA:UniProtKB.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:UniProtKB.
DR Gene3D; 2.60.120.590; -; 1.
DR InterPro; IPR027450; AlkB-like.
DR InterPro; IPR037151; AlkB-like_sf.
DR InterPro; IPR044842; ALKBH9B/ALKBH10B-like.
DR InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
DR PANTHER; PTHR31447; PTHR31447; 1.
DR Pfam; PF13532; 2OG-FeII_Oxy_2; 1.
DR PROSITE; PS51471; FE2OG_OXY; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Dioxygenase; Host-virus interaction; Iron; Metal-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..507
FT /note="RNA demethylase ALKBH9B"
FT /id="PRO_0000445522"
FT DOMAIN 317..414
FT /note="Fe2OG dioxygenase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT REGION 76..102
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 145..183
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 432..507
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 83..100
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 145..159
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 160..183
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 438..461
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 335
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 337
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 396
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 405
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
SQ SEQUENCE 507 AA; 57427 MW; B073165433A764CF CRC64;
MENDPFLRQY QPSELKIASE FLTNWLPFLS KDLCKDCNHL LSNRIRSLDP AHCSNNTDKV
DGECKTGSCS VVENMGSERA SNNVDDNYDE KSENGEDCDN HSLGSWKGSE IVFGSFPEDF
SSVLQSRPAV VETASPRMRW ADMAQEDEFD EEEEEEEEER DSSRKGFDAS SMKTPEKPKL
SRDQRENLRL INVKRKKDFI CLERVKGKIV NVLDGLELHT GVFSAVEQKR IVDQVYQLQE
KGRRGELKKR TFTAPHKWMR GKGRETIQFG CCYNYAPDRA GNPPGILQRE EVDPLPHLFK
VIIRKLIKWH VLPPTCVPDS CIVNIYDEGD CIPPHIDNHD FLRPFCTISF LSECDILFGS
NLKVEGPGDF SGSYSIPLPV GSVLVLNGNG ADVAKHCVPA VPTKRISITF RKMDESKRPV
WFTPEPDLQG IEPLPLDLNR SGSTSRFSRL NNHNGTNQRG HGRRGGGNGY DSRGYYNPER
SSEHNDSGDW PSSQRRGMPR PSRRNYG
