ID DEXHC_ARATH Reviewed; 2171 AA.
AC Q9SYP1; Q56Z02; Q8W577;
DT 20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 166.
DE RecName: Full=DExH-box ATP-dependent RNA helicase DExH12 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000305};
DE AltName: Full=BRR2 homolog A {ECO:0000305};
DE Short=AtBRR2A {ECO:0000303|PubMed:19261069};
DE AltName: Full=Pre-mRNA-splicing helicase BRR2A {ECO:0000305};
DE AltName: Full=Protein EMBRYO DEFECTIVE 1507 {ECO:0000303|PubMed:15266054};
GN Name=BRR2A {ECO:0000303|PubMed:19261069};
GN Synonyms=EMB1507 {ECO:0000303|PubMed:15266054};
GN OrderedLocusNames=At1g20960 {ECO:0000312|Araport:AT1G20960};
GN ORFNames=F9H16.5 {ECO:0000312|EMBL:AAD30595.1};
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] OF 1600-2171.
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] OF 2122-2171.
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 IDENTIFICATION, AND DISRUPTION PHENOTYPE.
RX PubMed=15266054; DOI=10.1104/pp.104.045179;
RA Tzafrir I., Pena-Muralla R., Dickerman A., Berg M., Rogers R., Hutchens S.,
RA Sweeney T.C., McElver J., Aux G., Patton D., Meinke D.;
RT "Identification of genes required for embryo development in Arabidopsis.";
RL Plant Physiol. 135:1206-1220(2004).
RN [6]
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).
RN [7]
RP INTERACTION WITH CLO.
RX PubMed=19261069; DOI=10.1111/j.1744-7909.2008.00783.x;
RA Liu M., Yuan L., Liu N.Y., Shi D.Q., Liu J., Yang W.C.;
RT "GAMETOPHYTIC FACTOR 1, involved in pre-mRNA splicing, is essential for
RT megagametogenesis and embryogenesis in Arabidopsis.";
RL J. Integr. Plant Biol. 51:261-271(2009).
CC -!- FUNCTION: RNA helicase that plays an essential role in pre-mRNA
CC splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes.
CC Involved in spliceosome assembly, activation and disassembly.
CC {ECO:0000250|UniProtKB:P32639}.
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 Evidence={ECO:0000305};
CC -!- SUBUNIT: Interacts with CLO. {ECO:0000269|PubMed:19261069}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Embryo defective. {ECO:0000269|PubMed:15266054}.
CC -!- SIMILARITY: Belongs to the DExH box helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL31915.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC007369; AAD30595.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30046.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30047.1; -; Genomic_DNA.
DR EMBL; AF419583; AAL31915.1; ALT_INIT; mRNA.
DR EMBL; AY113040; AAM47348.1; -; mRNA.
DR EMBL; AK221168; BAD95221.1; -; mRNA.
DR PIR; E86342; E86342.
DR RefSeq; NP_001185050.1; NM_001198121.1.
DR RefSeq; NP_173520.1; NM_101949.5.
DR AlphaFoldDB; Q9SYP1; -.
DR SMR; Q9SYP1; -.
DR IntAct; Q9SYP1; 6.
DR MINT; Q9SYP1; -.
DR STRING; 3702.Q9SYP1; -.
DR iPTMnet; Q9SYP1; -.
DR PaxDb; 3702-AT1G20960-1; -.
DR ProteomicsDB; 224623; -.
DR EnsemblPlants; AT1G20960.1; AT1G20960.1; AT1G20960.
DR EnsemblPlants; AT1G20960.2; AT1G20960.2; AT1G20960.
DR GeneID; 838690; -.
DR Gramene; AT1G20960.1; AT1G20960.1; AT1G20960.
DR Gramene; AT1G20960.2; AT1G20960.2; AT1G20960.
DR KEGG; ath:AT1G20960; -.
DR Araport; AT1G20960; -.
DR TAIR; AT1G20960; EMB1507.
DR eggNOG; KOG0951; Eukaryota.
DR HOGENOM; CLU_000335_1_0_1; -.
DR InParanoid; Q9SYP1; -.
DR OMA; QTEIQYY; -.
DR OrthoDB; 57056at2759; -.
DR PhylomeDB; Q9SYP1; -.
DR PRO; PR:Q9SYP1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SYP1; baseline and differential.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0006397; P:mRNA processing; IMP:TAIR.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:TAIR.
DR CDD; cd18019; DEXHc_Brr2_1; 1.
DR CDD; cd18021; DEXHc_Brr2_2; 1.
DR CDD; cd18795; SF2_C_Ski2; 2.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2.
DR Gene3D; 2.60.40.150; C2 domain; 2.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 4.
DR Gene3D; 1.10.3380.10; Sec63 N-terminal domain-like domain; 2.
DR Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 2.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR041094; Brr2_helicase_PWI.
DR InterPro; IPR048863; BRR2_plug.
DR InterPro; IPR035892; C2_domain_sf.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR014756; Ig_E-set.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR004179; Sec63-dom.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR PANTHER; PTHR47961; DNA POLYMERASE THETA, PUTATIVE (AFU_ORTHOLOGUE AFUA_1G05260)-RELATED; 1.
DR PANTHER; PTHR47961:SF4; U5 SMALL NUCLEAR RIBONUCLEOPROTEIN HELICASE; 1.
DR Pfam; PF21188; BRR2_plug; 1.
DR Pfam; PF00270; DEAD; 2.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF18149; Helicase_PWI; 1.
DR Pfam; PF02889; Sec63; 2.
DR PIRSF; PIRSF039073; BRR2; 1.
DR SMART; SM00382; AAA; 2.
DR SMART; SM00487; DEXDc; 2.
DR SMART; SM00490; HELICc; 2.
DR SMART; SM00973; Sec63; 2.
DR SUPFAM; SSF81296; E set domains; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 4.
DR SUPFAM; SSF158702; Sec63 N-terminal domain-like; 2.
DR SUPFAM; SSF46785; Winged helix' DNA-binding domain; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 2.
DR PROSITE; PS51194; HELICASE_CTER; 2.
PE 1: Evidence at protein level;
KW ATP-binding; Helicase; Hydrolase; mRNA processing; mRNA splicing;
KW Nucleotide-binding; Nucleus; Reference proteome; Repeat; RNA-binding;
KW Spliceosome.
FT CHAIN 1..2171
FT /note="DExH-box ATP-dependent RNA helicase DExH12"
FT /id="PRO_0000435299"
FT DOMAIN 514..697
FT /note="Helicase ATP-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 731..941
FT /note="Helicase C-terminal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 1006..1308
FT /note="SEC63 1"
FT /evidence="ECO:0000255"
FT DOMAIN 1360..1537
FT /note="Helicase ATP-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 1574..1779
FT /note="Helicase C-terminal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 1839..2157
FT /note="SEC63 2"
FT /evidence="ECO:0000255"
FT REGION 24..80
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 218..267
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 383..426
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 639..642
FT /note="DEIH box"
FT /evidence="ECO:0000305"
FT MOTIF 1479..1482
FT /note="DELH box"
FT /evidence="ECO:0000305"
FT COMPBIAS 54..80
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 218..243
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 527..534
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1373..1380
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 2122..2124
FT /note="KVK -> EVR (in Ref. 4; BAD95221)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 2171 AA; 247105 MW; 6D40D04E080574B6 CRC64;
MANLGGGAEA HARFKQYEYR ANSSLVLTTD NRPRDTHEPT GEPETLWGKI DPRSFGDRVA
KGRPQELEDK LKKSKKKERD VVDDMVNIRQ SKRRRLREES VLTDTDDAVY QPKTKETRAA
YEAMLGLIQK QLGGQPPSIV SGAADEILAV LKNDAFRNPE KKMEIEKLLN KIENHEFDQL
VSIGKLITDF QEGGDSGGGR ANDDEGLDDD LGVAVEFEEN EEDDEESDPD MVEEDDDEED
DEPTRTGGMQ VDAGINDEDA GDANEGTNLN VQDIDAYWLQ RKISQAYEQQ IDPQQCQVLA
EELLKILAEG DDRVVEDKLL MHLQYEKFSL VKFLLRNRLK VVWCTRLARA EDQEERNRIE
EEMRGLGPEL TAIVEQLHAT RATAKEREEN LQKSINEEAR RLKDETGGDG GRGRRDVADR
DSESGWVKGQ RQMLDLESLA FDQGGLLMAN KKCDLPPGSY RSHGKGYDEV HVPWVSKKVD
RNEKLVKITE MPDWAQPAFK GMQQLNRVQS KVYDTALFKA ENILLCAPTG AGKTNVAMLT
ILQQLEMNRN TDGTYNHGDY KIVYVAPMKA LVAEVVGNLS NRLKDYGVIV RELSGDQSLT
GREIEETQII VTTPEKWDII TRKSGDRTYT QLVRLLIIDE IHLLHDNRGP VLESIVARTL
RQIETTKENI RLVGLSATLP NYEDVALFLR VDLKKGLFKF DRSYRPVPLH QQYIGISVKK
PLQRFQLMND LCYQKVLAGA GKHQVLIFVH SRKETSKTAR AIRDTAMAND TLSRFLKEDS
VTRDVLHSHE DIVKNSDLKD ILPYGFAIHH AGLSRGDREI VETLFSQGHV QVLVSTATLA
WGVNLPAHTV IIKGTQVYNP EKGAWMELSP LDVMQMLGRA GRPQYDQHGE GIIITGYSEL
QYYLSLMNEQ LPIESQFISK LADQLNAEIV LGTVQNAREA CHWLGYTYLY IRMVRNPTLY
GLAPDALAKD VVLEERRADL IHSAATILDK NNLVKYDRKS GYFQVTDLGR IASYYYITHG
TIATYNEHLK PTMGDIDLYR LFSLSDEFKY VTVRQDEKME LAKLLDRVPI PIKETLEEPS
AKINVLLQAY ISQLKLEGLS LTSDMVYITQ SAGRLVRALY EIVLKRGWAQ LAEKALNLSK
MVGKRMWSVQ TPLRQFHGLS NDILMQLEKK DLVWERYYDL SAQELGELIR SPKMGKPLHK
FIHQFPKVTL SAHVQPITRT VLNVELTVTP DFLWDEKIHK YVEPFWIIVE DNDGEKILHH
EYFLLKKQYI DEDHTLHFTV PIFEPLPPQY FVRVVSDKWL GSETVLPVSF RHLILPEKYP
PPTELLDLQP LPVTALRNPN YEILYQDFKH FNPVQTQVFT VLYNTNDNVL VAAPTGSGKT
ICAEFAILRN HHEGPDATMR VVYIAPLEAI AKEQFRIWEG KFGKGLGLRV VELTGETALD
LKLLEKGQII ISTPEKWDAL SRRWKQRKYV QQVSLFIVDE LHLIGGQHGP VLEVIVSRMR
YISSQVINKI RIVALSTSLA NAKDLGEWIG ASSHGLFNFP PGVRPVPLEI HIQGVDISSF
EARMQAMTKP TYTAIVQHAK NKKPAIVFVP TRKHVRLTAV DLMAYSHMDN PQSPDFLLGK
LEELDPFVEQ IREETLKETL CHGIGYLHEG LSSLDQEIVT QLFEAGRIQV CVMSSSLCWG
TPLTAHLVVV MGTQYYDGRE NSHSDYPVPD LLQMMGRASR PLLDNAGKCV IFCHAPRKEY
YKKFLYEAFP VESQLQHFLH DNFNAEVVAG VIENKQDAVD YLTWTFMYRR LPQNPNYYNL
QGVSHRHLSD HLSELVENTL SDLEASKCIE VEDEMELSPL NLGMIASYYY ISYTTIERFS
SLLSSKTKMK GLLEILTSAS EYDMIPIRPG EEDTVRRLIN HQRFSFENPK CTDPHVKANA
LLQAHFSRQN IGGNLAMDQR DVLLSATRLL QAMVDVISSN GWLNLALLAM EVSQMVTQGM
WERDSMLLQL PHFTKDLAKR CQENPGKNIE TVFDLVEMED EERQELLKMS DAQLLDIARF
CNRFPNIDLT YEIVGSEEVN PGKEVTLQVM LERDMEGRTE VGPVDSLRYP KTKEEGWWLV
VGDTKTNQLL AIKRVSLQRK VKVKLDFTAP SEPGEKSYTL YFMCDSYLGC DQEYSFSVDV
KGSGAGDRME E
//
