RH3B_MAIZE
ID RH3B_MAIZE Reviewed; 743 AA.
AC A0A1D6LAB7; B4FA24; B6SSK6;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2016, sequence version 1.
DT 03-AUG-2022, entry version 32.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 3B, chloroplastic {ECO:0000305};
DE Short=ZmRH3B {ECO:0000303|PubMed:22576849};
DE EC=3.6.4.13 {ECO:0000305};
DE Flags: Precursor;
GN Name=RH3B {ECO:0000303|PubMed:22576849};
GN ORFNames=ZEAMMB73_Zm00001d034721 {ECO:0000312|EMBL:ONM11072.1};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. B73;
RX PubMed=19965430; DOI=10.1126/science.1178534;
RA Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S.,
RA Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D.,
RA Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K.,
RA Fronick C., Courtney B., Rock S.M., Belter E., Du F., Kim K., Abbott R.M.,
RA Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M., Gillam B.,
RA Chen W., Yan L., Higginbotham J., Cardenas M., Waligorski J., Applebaum E.,
RA Phelps L., Falcone J., Kanchi K., Thane T., Scimone A., Thane N., Henke J.,
RA Wang T., Ruppert J., Shah N., Rotter K., Hodges J., Ingenthron E.,
RA Cordes M., Kohlberg S., Sgro J., Delgado B., Mead K., Chinwalla A.,
RA Leonard S., Crouse K., Collura K., Kudrna D., Currie J., He R.,
RA Angelova A., Rajasekar S., Mueller T., Lomeli R., Scara G., Ko A.,
RA Delaney K., Wissotski M., Lopez G., Campos D., Braidotti M., Ashley E.,
RA Golser W., Kim H., Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A.,
RA Fan C., Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T.,
RA Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L.,
RA Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Van Buren P.,
RA Vaughn M.W., Ying K., Yeh C.-T., Emrich S.J., Jia Y., Kalyanaraman A.,
RA Hsia A.-P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C.,
RA Chaparro C., Chia J.-M., Deragon J.-M., Estill J.C., Fu Y., Jeddeloh J.A.,
RA Han Y., Lee H., Li P., Lisch D.R., Liu S., Liu Z., Nagel D.H., McCann M.C.,
RA SanMiguel P., Myers A.M., Nettleton D., Nguyen J., Penning B.W.,
RA Ponnala L., Schneider K.L., Schwartz D.C., Sharma A., Soderlund C.,
RA Springer N.M., Sun Q., Wang H., Waterman M., Westerman R., Wolfgruber T.K.,
RA Yang L., Yu Y., Zhang L., Zhou S., Zhu Q., Bennetzen J.L., Dawe R.K.,
RA Jiang J., Jiang N., Presting G.G., Wessler S.R., Aluru S.,
RA Martienssen R.A., Clifton S.W., McCombie W.R., Wing R.A., Wilson R.K.;
RT "The B73 maize genome: complexity, diversity, and dynamics.";
RL Science 326:1112-1115(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=18937034; DOI=10.1007/s11103-008-9415-4;
RA Alexandrov N.N., Brover V.V., Freidin S., Troukhan M.E., Tatarinova T.V.,
RA Zhang H., Swaller T.J., Lu Y.-P., Bouck J., Flavell R.B., Feldmann K.A.;
RT "Insights into corn genes derived from large-scale cDNA sequencing.";
RL Plant Mol. Biol. 69:179-194(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 10-743.
RC STRAIN=cv. B73;
RX PubMed=19936069; DOI=10.1371/journal.pgen.1000740;
RA Soderlund C., Descour A., Kudrna D., Bomhoff M., Boyd L., Currie J.,
RA Angelova A., Collura K., Wissotski M., Ashley E., Morrow D., Fernandes J.,
RA Walbot V., Yu Y.;
RT "Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.";
RL PLoS Genet. 5:E1000740-E1000740(2009).
RN [4]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=22576849; DOI=10.1104/pp.112.197525;
RA Asakura Y., Galarneau E., Watkins K.P., Barkan A., van Wijk K.J.;
RT "Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function
RT in splicing of specific group II introns and affect chloroplast ribosome
RT biogenesis.";
RL Plant Physiol. 159:961-974(2012).
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=25725436; DOI=10.1016/j.bbabio.2015.02.014;
RA Belcher S., Williams-Carrier R., Stiffler N., Barkan A.;
RT "Large-scale genetic analysis of chloroplast biogenesis in maize.";
RL Biochim. Biophys. Acta 1847:1004-1016(2015).
CC -!- FUNCTION: Nuclear genome-encoded factor involved in ribosome biogenesis
CC in chloroplasts. Binds specific group II introns in chloroplasts and
CC facilitates their splicing. Is required for rRNA maturation in plastids
CC and may contribute to the assembly of the large (50S) ribosomal
CC subunit. Required for normal development of chloroplasts.
CC {ECO:0000269|PubMed:22576849}.
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 -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:22576849}.
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 {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Very pale yellow green leaf phenotype. Virescent
CC leaf phenotype. {ECO:0000269|PubMed:25725436}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX21/DDX50
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ACF78967.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; CM007647; ONM11072.1; -; Genomic_DNA.
DR EMBL; EU955721; ACG27839.1; -; mRNA.
DR EMBL; BT033962; ACF78967.1; ALT_INIT; mRNA.
DR RefSeq; NP_001130659.1; NM_001137187.1.
DR RefSeq; XP_008671379.1; XM_008673157.1.
DR AlphaFoldDB; A0A1D6LAB7; -.
DR SMR; A0A1D6LAB7; -.
DR STRING; 4577.AC198418.3_FGP005; -.
DR EnsemblPlants; Zm00001eb063300_T001; Zm00001eb063300_P001; Zm00001eb063300.
DR GeneID; 100191761; -.
DR Gramene; Zm00001eb063300_T001; Zm00001eb063300_P001; Zm00001eb063300.
DR KEGG; zma:100191761; -.
DR eggNOG; KOG0331; Eukaryota.
DR OMA; IQYFIPA; -.
DR OrthoDB; 1139373at2759; -.
DR Proteomes; UP000007305; Chromosome 1.
DR ExpressionAtlas; A0A1D6LAB7; baseline and differential.
DR GO; GO:0009570; C:chloroplast stroma; IDA:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; 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 GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009658; P:chloroplast organization; IMP:UniProtKB.
DR GO; GO:0000373; P:Group II intron splicing; IMP:UniProtKB.
DR GO; GO:0042254; P:ribosome biogenesis; IMP:UniProtKB.
DR GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR012562; GUCT.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF08152; GUCT; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00098; zf-CCHC; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF57756; SSF57756; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Chloroplast; Helicase; Hydrolase; Metal-binding;
KW Nucleotide-binding; Plastid; Reference proteome; Ribosome biogenesis;
KW RNA-binding; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..37
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 38..743
FT /note="DEAD-box ATP-dependent RNA helicase 3B,
FT chloroplastic"
FT /id="PRO_0000441333"
FT DOMAIN 119..295
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 324..469
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 725..742
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 60..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 606..719
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 88..116
FT /note="Q motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00552"
FT MOTIF 243..246
FT /note="DEAD box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 651..683
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 684..719
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 132..139
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 318
FT /note="T -> A (in Ref. 2; ACG27839)"
FT /evidence="ECO:0000305"
FT CONFLICT 695
FT /note="R -> RS (in Ref. 2; ACG27839)"
FT /evidence="ECO:0000305"
FT CONFLICT 716
FT /note="G -> S (in Ref. 2; ACG27839)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 743 AA; 80171 MW; 3A2BB60A110B1E69 CRC64;
MASLTLPALA LALSNPGAVR LRAAAFRCWA LRRRGWAAAG ALASPNSVLS EHAFKRLQLG
SDDEDGEGPY GSDADEGFEA GEGDNEELAI ARLGLPDELV ATLEKRGITH LFPIQRAVLI
PALEGRDLIA RAKTGTGKTL AFGIPMIKQL IEQDDGRITR RGRTPRVLVL APTRELAKQV
EKEIKESAPK LGTVCVYGGV SYNVQQNALS RGVDVVVGTP GRIIDLINGG SLQLGEVQYL
VLDEADQMLA VGFEEDVETI LQQLPAGRQS MLFSATMPSW VKKLSRRYLN NPLTIDLVGD
QDEKLAEGIK LYAIPLTTTS KRTVLSDLIT VYAKGGKTIV FTRTKKDADE VSLALTNSIA
SEALHGDISQ HQRERTLNGF RQGKFTVLVA TDVAARGLDI PNVDLIIHYE LPNDPETFVH
RSGRTGRAGK AGTAILMFTS SQKRTVKSLE RDVGCNFEFI SPPSIEEVLE SSAEHVIATL
RGVHPESTKY FLGAAEKLTE ELGPHALASA LAHLSGFSQP PSSRSLISHE QGWVTLQLTR
EQGFGRGFFS PRSVTGFLSD VCSAAADEVG KIYLTADENV QGAVFDLPEE IAKDLLTMEL
PPGNTLTKIS KLPALQDDGP ATDSYGRFSN DRGSRNNRRS RGGGASRGRG GWDTDGEDRF
RRGGRSLRSD NDSWSDDDWS GGGRKSNRSS SFGSRSSSYS SRGSPSFGGR SSSFGGRESN
RSFSGACFNC GESGHRATDC PNK
