RH13_ARATH
ID RH13_ARATH Reviewed; 826 AA.
AC Q93Y39; C0Z292; F4J3W8; Q94AW1; Q9LRY9; Q9ZS07;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 25-JAN-2012, sequence version 3.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 13;
DE EC=3.6.4.13;
GN Name=RH13; OrderedLocusNames=At3g16840; ORFNames=K20I9.7;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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].
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-797.
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 [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 331-802.
RC STRAIN=cv. Columbia;
RX PubMed=9862990; DOI=10.1093/nar/27.2.628;
RA Aubourg S., Kreis M., Lecharny A.;
RT "The DEAD box RNA helicase family in Arabidopsis thaliana.";
RL Nucleic Acids Res. 27:628-636(1999).
RN [6]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17168887; DOI=10.1111/j.1467-7652.2004.00084.x;
RA Mingam A., Toffano-Nioche C., Brunaud V., Boudet N., Kreis M., Lecharny A.;
RT "DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link
RT between quantitative expression, gene structure and evolution of a family
RT of genes.";
RL Plant Biotechnol. J. 2:401-415(2004).
RN [7]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX24/MAK5
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA95778.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA09204.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AB028608; BAA95778.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE75872.1; -; Genomic_DNA.
DR EMBL; AK318706; BAH56821.1; -; mRNA.
DR EMBL; AY045669; AAK74027.1; -; mRNA.
DR EMBL; AY054475; AAK96666.1; -; mRNA.
DR EMBL; AJ010465; CAA09204.1; ALT_FRAME; mRNA.
DR PIR; T51744; T51744.
DR RefSeq; NP_188307.3; NM_112558.6.
DR AlphaFoldDB; Q93Y39; -.
DR SMR; Q93Y39; -.
DR BioGRID; 6271; 1.
DR STRING; 3702.AT3G16840.1; -.
DR iPTMnet; Q93Y39; -.
DR PaxDb; Q93Y39; -.
DR PRIDE; Q93Y39; -.
DR EnsemblPlants; AT3G16840.1; AT3G16840.1; AT3G16840.
DR GeneID; 820937; -.
DR Gramene; AT3G16840.1; AT3G16840.1; AT3G16840.
DR KEGG; ath:AT3G16840; -.
DR Araport; AT3G16840; -.
DR TAIR; locus:2086775; AT3G16840.
DR eggNOG; KOG0347; Eukaryota.
DR HOGENOM; CLU_003041_13_0_1; -.
DR InParanoid; Q93Y39; -.
DR OMA; HYHVPRT; -.
DR PRO; PR:Q93Y39; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q93Y39; baseline and differential.
DR Genevisible; Q93Y39; AT.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Coiled coil; Helicase; Hydrolase; Nucleotide-binding;
KW Reference proteome; RNA-binding.
FT CHAIN 1..826
FT /note="DEAD-box ATP-dependent RNA helicase 13"
FT /id="PRO_0000239155"
FT DOMAIN 222..439
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 476..644
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..62
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 76..175
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 783..826
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 125..166
FT /evidence="ECO:0000255"
FT COILED 666..712
FT /evidence="ECO:0000255"
FT COILED 783..810
FT /evidence="ECO:0000255"
FT MOTIF 190..218
FT /note="Q motif"
FT MOTIF 363..366
FT /note="DEAD box"
FT COMPBIAS 97..128
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 135..156
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 785..812
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 235..242
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 166
FT /note="S -> SA (in Ref. 3; BAH56821)"
FT /evidence="ECO:0000305"
FT CONFLICT 389
FT /note="K -> R (in Ref. 3; BAH56821)"
FT /evidence="ECO:0000305"
FT CONFLICT 580
FT /note="P -> Q (in Ref. 3; BAH56821)"
FT /evidence="ECO:0000305"
FT CONFLICT 653
FT /note="E -> D (in Ref. 5; CAA09204)"
FT /evidence="ECO:0000305"
FT CONFLICT 802
FT /note="R -> K (in Ref. 5; CAA09204)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 826 AA; 93986 MW; 680994BE37F4B2B1 CRC64;
MVTGDKESSL MKKRNKRSHK RKREEDFERI DSLPWSSSIP IGEDDEGESF STLFSGSGQL
DGGFLSLEEI DEADYHLTLP TIESEITERK QSPEDDDDTN ETVDEMIEGE EAEEDGEGRD
DEDDEDDEET RKKKEKKAKR NKEKKKEKKK KKQKKINEAA KNQDASAVSC DGDDTVEEQV
EEEEIPPEFS AWSSMRLHPL LMKSIYRLDF KEPTKIQKAC FNVAAYQGKD VIGAAETGSG
KTLAFGLPIL QRLLDEREKV GKLYALKGEE AQKYAADGYL RALIITPTRE LALQVTEHLE
NAAKNLSVKV VPIVGGMFSE KQERRLKEKP EIVVATPGRL WELMSAGEKH LVELHSLSFF
VLDEADRMVE RGHFRELQSI LDLLPVTDKP NEGKTQTVKS NDTVLNVPKK KRQTFVFSAT
IALSSDFRKK LKRGSSKSKQ SSSGEVNSIE VLSERAGMRD NVAIIDLTTT SILAPKIEES
FIKCEEKEKD AYLYYILSVH GQGRTIVFCT SVTDLRHISG LLKILGLDVC TLFSEMKQRA
RLKSIDRFRA SENGILIATD LVARGIDIKN VRTIIHYKLP HSAEVYVHRC GRTARAFADG
CSIALIEPNE TSKFYTLCKS FSMESVKIFP LDNSYMPAVR KRLYLARQIY EIERKGSREN
ADRTWLKKHA ESMELELDDE ESEEERVDNV RQRKATSARL NKLKEELSTL LSHPMQPKKF
SGRYFAGVGV STLMQNQFVE LKKQKQAQMQ IGGDIKRRKL VVINQNCIEP LQALRAGGNE
MLKMKGQSAE KRRDIASLKK KRKEEKIGRR DQRRNQKKQR KLMASS
