RH40_ARATH
ID RH40_ARATH Reviewed; 1088 AA.
AC Q9SQV1;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 40;
DE EC=3.6.4.13;
GN Name=RH40; OrderedLocusNames=At3g06480; ORFNames=F24P17.2;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 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 [4]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [5]
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 -!- FUNCTION: ATP-dependent RNA helicase involved nonsense-mediated mRNA
CC decay and ribosome biogenesis through rRNA processing. {ECO:0000250}.
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
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. DDX5/DBP2
CC subfamily. {ECO:0000305}.
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DR EMBL; AC011623; AAF08584.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74400.1; -; Genomic_DNA.
DR RefSeq; NP_187299.1; NM_111523.3.
DR AlphaFoldDB; Q9SQV1; -.
DR SMR; Q9SQV1; -.
DR BioGRID; 5160; 3.
DR STRING; 3702.AT3G06480.1; -.
DR iPTMnet; Q9SQV1; -.
DR PaxDb; Q9SQV1; -.
DR PRIDE; Q9SQV1; -.
DR ProteomicsDB; 236890; -.
DR EnsemblPlants; AT3G06480.1; AT3G06480.1; AT3G06480.
DR GeneID; 819825; -.
DR Gramene; AT3G06480.1; AT3G06480.1; AT3G06480.
DR KEGG; ath:AT3G06480; -.
DR Araport; AT3G06480; -.
DR TAIR; locus:2081061; AT3G06480.
DR eggNOG; KOG0331; Eukaryota.
DR HOGENOM; CLU_003041_31_0_1; -.
DR InParanoid; Q9SQV1; -.
DR OMA; YPINALM; -.
DR OrthoDB; 638613at2759; -.
DR PhylomeDB; Q9SQV1; -.
DR PRO; PR:Q9SQV1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SQV1; baseline and differential.
DR Genevisible; Q9SQV1; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:1990904; C:ribonucleoprotein complex; 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; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR CDD; cd00201; WW; 1.
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 InterPro; IPR001202; WW_dom.
DR InterPro; IPR036020; WW_dom_sf.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00397; WW; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00456; WW; 1.
DR SUPFAM; SSF51045; SSF51045; 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.
DR PROSITE; PS01159; WW_DOMAIN_1; 1.
DR PROSITE; PS50020; WW_DOMAIN_2; 1.
PE 2: Evidence at transcript level;
KW Acetylation; ATP-binding; Helicase; Hydrolase;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus;
KW Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..1088
FT /note="DEAD-box ATP-dependent RNA helicase 40"
FT /id="PRO_0000239180"
FT DOMAIN 20..54
FT /note="WW"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 466..640
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 669..813
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 47..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 192..254
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 861..1033
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 435..463
FT /note="Q motif"
FT MOTIF 588..591
FT /note="DEAD box"
FT COMPBIAS 65..178
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..220
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 238..254
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 944..967
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 973..987
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 988..1007
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 479..486
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 1088 AA; 119556 MW; E536499CDCA48DFC CRC64;
MATTEDTPAS AGPRYAPEDP TLPQPWKGLI DGSTGILYYW NPETNVTQYE RPSAPPPHSA
TTPKLAQIPV PSSGQGHQAQ HEQAKPVGHV SQQHGFQQQP QQFPSQHVRP QMMQQHPAQQ
MPQQSGQQFP QQQSQSMVPH PHGHPSVQTY QPTTQQQQQG MQNQHSQMPQ QLSHQYAHSQ
QHYMGFRPHM QTQGLQNSHQ TPQGGPHGQQ FPSQQEYNSL APKREGDEFH GGKKTGFSQP
HLPNSERSPS QNTHFEANAA SQKTNANLAM AQKCNGPQAN AAVTQFQQPG ANLIHQQLGP
RAPNQMDQTM LHQKSHVSPF QSNNTYENNL QSRPGNDSYV NMRMEVPVRG AQPLHPAAMP
KDIRISGGPP TNADPAMGQT GHGTYGHAGP AFPNKSLVRP HFVTSPDVPH LSPVEIYRKQ
HEVTTTGENI PAPYITFESS GLPPEILREL LSAGFPSPTP IQAQTWPIAL QSRDIVAIAK
TGSGKTLGYL IPAFILLRHC RNDSRNGPTV LILAPTRELA TQIQDEALRF GRSSRISCTC
LYGGAPKGPQ LKELERGADI VVATPGRLND ILEMKMIDFQ QVSLLVLDEA DRMLDMGFEP
QIRKIVNEIP PRRQTLMYTA TWPKEVRKIA SDLLVNPVQV NIGRVDELAA NKAITQYVEV
VPQMEKERRL EQILRSQERG SKVIIFCSTK RLCDHLARSV GRHFGAVVIH GDKTQGERDW
VLNQFRSGKS CVLIATDVAA RGLDIKDIRV VINYDFPTGV EDYVHRIGRT GRAGATGVAF
TFFTEQDWKY APDLIKVLEG ANQQVPPQVR DIAMRGGGGG GPGYSQDRRG MVNRFDSGGG
GTRWDSGGGF GGRGGGFSGR EGGFGGREGG FGGREGGFGG RGGRFGMRDD SFGRGGNRGR
GFTGPDAGHM NVGGRGGFGR FGNNNNMESR GFGRGSGRGF GRGVGRFDNR RGRSRSRSPD
LVRPRRRSSS YSRSRSRSGS YSRSRSRSRS WSRSRSRSPR HSRDRGGHNR SRSYSRSPSP
VYERRDRAPR VSGFDIKPPV ESVVNLDMNA AAAIENVVPT SLSERQGNGV VESEVEAALV
RPVVDEEP
