ALKB8_ARATH
ID ALKB8_ARATH Reviewed; 346 AA.
AC Q8RWY1; A0A1P8ATR1; Q56YW5; Q9C6V1;
DT 31-JAN-2018, integrated into UniProtKB/Swiss-Prot.
DT 31-JAN-2018, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Alkylated DNA repair protein ALKBH8 homolog {ECO:0000305};
DE EC=1.14.11.- {ECO:0000305};
DE AltName: Full=Alpha-ketoglutarate-dependent dioxygenase ALKBH8 homolog {ECO:0000305};
DE Short=AtALKBH8 {ECO:0000303|PubMed:21653555};
GN Name=ALKBH8 {ECO:0000303|PubMed:21653555};
GN OrderedLocusNames=At1g31600 {ECO:0000312|Araport:AT1G31600};
GN ORFNames=F27M3_19 {ECO:0000312|EMBL:AAG60147.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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] (ISOFORM 2).
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] (ISOFORM 2).
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND ALTERNATIVE SPLICING.
RX PubMed=21653555; DOI=10.1093/nar/gkr406;
RA Leihne V., Kirpekar F., Vaagboe C.B., van den Born E., Krokan H.E.,
RA Grini P.E., Meza T.J., Falnes P.O.;
RT "Roles of Trm9- and ALKBH8-like proteins in the formation of modified
RT wobble uridines in Arabidopsis tRNA.";
RL Nucleic Acids Res. 39:7688-7701(2011).
CC -!- FUNCTION: Binds tRNA and catalyzes the iron and alpha-ketoglutarate
CC dependent hydroxylation of 5-methylcarboxymethyl uridine at the wobble
CC position of the anticodon loop in tRNA via its dioxygenase domain,
CC giving rise to 5-(S)-methoxycarbonylhydroxymethyluridine.
CC {ECO:0000269|PubMed:21653555}.
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8RWY1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8RWY1-2; Sequence=VSP_059310;
CC -!- MISCELLANEOUS: [Isoform 2]: Arabidopsis ALKB8 isoform 2 has an
CC extension of 83 amino acids in its N-terminus, but this extension
CC shares no detectable sequence homology with other plant orthologs. The
CC 159 nucleotide DNA sequence encoding the N-terminal part (53 amino
CC acids) of the 83 amino acid extension is highly similar (94% sequence
CC identity) to the Ac-type transposon Tag2.
CC {ECO:0000305|PubMed:21653555}.
CC -!- SIMILARITY: Belongs to the alkB family. {ECO:0000305}.
CC -!- CAUTION: Arabidopsis ALKB8 isoform 2 has an extension of 83 amino acids
CC in its N-terminus, but this extension shares no detectable sequence
CC homology with other plant orthologs. The 159 nucleotide DNA sequence
CC encoding the N-terminal part (53 amino acids) of the 83 amino acid
CC extension is highly similar (94% sequence identity) to the Ac-type
CC transposon Tag2. {ECO:0000305|PubMed:21653555}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG60147.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC074360; AAG60147.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE31374.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31376.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60042.1; -; Genomic_DNA.
DR EMBL; AY091033; AAM13854.1; -; mRNA.
DR EMBL; AY133725; AAM91659.1; -; mRNA.
DR EMBL; AK221205; BAD93744.1; -; mRNA.
DR RefSeq; NP_001322355.1; NM_001332970.1. [Q8RWY1-1]
DR RefSeq; NP_174442.2; NM_102896.3. [Q8RWY1-2]
DR RefSeq; NP_973946.1; NM_202217.1. [Q8RWY1-2]
DR AlphaFoldDB; Q8RWY1; -.
DR SMR; Q8RWY1; -.
DR STRING; 3702.AT1G31600.1; -.
DR PaxDb; Q8RWY1; -.
DR PRIDE; Q8RWY1; -.
DR EnsemblPlants; AT1G31600.1; AT1G31600.1; AT1G31600. [Q8RWY1-2]
DR EnsemblPlants; AT1G31600.3; AT1G31600.3; AT1G31600. [Q8RWY1-2]
DR EnsemblPlants; AT1G31600.4; AT1G31600.4; AT1G31600. [Q8RWY1-1]
DR GeneID; 840048; -.
DR Gramene; AT1G31600.1; AT1G31600.1; AT1G31600. [Q8RWY1-2]
DR Gramene; AT1G31600.3; AT1G31600.3; AT1G31600. [Q8RWY1-2]
DR Gramene; AT1G31600.4; AT1G31600.4; AT1G31600. [Q8RWY1-1]
DR KEGG; ath:AT1G31600; -.
DR Araport; AT1G31600; -.
DR TAIR; locus:2028631; AT1G31600.
DR eggNOG; KOG4176; Eukaryota.
DR InParanoid; Q8RWY1; -.
DR OMA; MEFRKYT; -.
DR OrthoDB; 996085at2759; -.
DR PhylomeDB; Q8RWY1; -.
DR PRO; PR:Q8RWY1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8RWY1; baseline and differential.
DR GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IMP:TAIR.
DR Gene3D; 2.60.120.590; -; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR027450; AlkB-like.
DR InterPro; IPR037151; AlkB-like_sf.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR Pfam; PF13532; 2OG-FeII_Oxy_2; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS51471; FE2OG_OXY; 1.
DR PROSITE; PS50102; RRM; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Dioxygenase; Iron; Metal-binding; Oxidoreductase;
KW Reference proteome; RNA-binding.
FT CHAIN 1..346
FT /note="Alkylated DNA repair protein ALKBH8 homolog"
FT /id="PRO_0000443080"
FT DOMAIN 24..102
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 208..328
FT /note="Fe2OG dioxygenase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 226
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 228
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 298
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000305"
FT BINDING 319
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 325
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q96BT7"
FT VAR_SEQ 1
FT /note="M -> MGWPWADHWTMVLNGLGQIFRPLSIKDQPLEPMKKMFQVDMTIGLWT
FT AQLTLLTQVNVIVFFIEHIGEDTSPLYDRRKLQSFIPRM (in isoform 2)"
FT /id="VSP_059310"
FT CONFLICT 59
FT /note="D -> E (in Ref. 4; BAD93744)"
FT /evidence="ECO:0000305"
FT CONFLICT 237
FT /note="I -> V (in Ref. 4; BAD93744)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 346 AA; 38424 MW; 334CCB2817D36FD2 CRC64;
MVQPRFVRPT QSSPSSISGE PNSSNLYVAN CGPAVGLTHN AIAAVFAEFG EVNGVYAADD
SGVRVIVSFA DPFSAKAALE ALSGRPCPDL KGRSLHIRYS VLQLPSETQV NDCVPVSLID
SELNIPGLFL LPDFVTVAEE QQLLAAVDAR HWIGLAKRRV QHYGYEFCYG TRNVDTKKRL
GELPSFVSPI LERIYLFPNF DNGSASLNLD QLTVNEYPSG VGLSPHIDTH SAFEDCIFSL
SLAGPCIMEF RRYSVSTWKA STTDAEKSGD SSCIKKALYL PPRSMLLLSG EARYAWNHYI
PHHKIDKVKD KVIRRSSRRV SFTLRKVRNH PCSCKYPQYC DSQQQM
