ELP3_ORYSJ
ID ELP3_ORYSJ Reviewed; 573 AA.
AC Q7X7L3; Q0JC95;
DT 04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Elongator complex protein 3 {ECO:0000305};
DE EC=2.3.1.- {ECO:0000250|UniProtKB:D5VRB9};
DE AltName: Full=Elongator component 3;
DE AltName: Full=tRNA uridine(34) acetyltransferase {ECO:0000305};
GN Name=ELP3; OrderedLocusNames=Os04g0484900, LOC_Os04g40840;
GN ORFNames=OJ000223_09.4, OSJNBa0081L15.14;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Catalytic tRNA acetyltransferase subunit of the elongator
CC complex which is required for multiple tRNA modifications, including
CC mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-
CC methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl
CC uridine) (By similarity). In the elongator complex, acts as a tRNA
CC uridine(34) acetyltransferase by mediating formation of
CC carboxymethyluridine in the wobble base at position 34 in tRNAs (By
CC similarity). {ECO:0000250|UniProtKB:D5VRB9,
CC ECO:0000250|UniProtKB:Q93ZR1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=acetyl-CoA + H2O + S-adenosyl-L-methionine + uridine(34) in
CC tRNA = 5'-deoxyadenosine + carboxymethyluridine(34) in tRNA + CoA + 2
CC H(+) + L-methionine; Xref=Rhea:RHEA:61020, Rhea:RHEA-COMP:10407,
CC Rhea:RHEA-COMP:11727, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:57287, ChEBI:CHEBI:57288,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:65315,
CC ChEBI:CHEBI:74882; Evidence={ECO:0000250|UniProtKB:D5VRB9};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61021;
CC Evidence={ECO:0000250|UniProtKB:D5VRB9};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:Q02908};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000250|UniProtKB:Q02908};
CC -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC biosynthesis. {ECO:0000250|UniProtKB:Q9H9T3}.
CC -!- SUBUNIT: Component of the elongator complex.
CC {ECO:0000250|UniProtKB:Q93ZR1}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ELP3 family. {ECO:0000305}.
CC -!- CAUTION: The elongator complex was originally thought to play a role in
CC transcription elongation. However, it is no longer thought to play a
CC direct role in this process and its primary function is thought to be
CC in tRNA modification. {ECO:0000250|UniProtKB:Q9H9T3}.
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DR EMBL; AL606623; CAE03152.2; -; Genomic_DNA.
DR EMBL; AL606998; CAE02005.2; -; Genomic_DNA.
DR EMBL; AP008210; BAF15042.1; -; Genomic_DNA.
DR EMBL; AP014960; BAS89780.1; -; Genomic_DNA.
DR EMBL; AK122179; BAH00832.1; -; mRNA.
DR RefSeq; XP_015635801.1; XM_015780315.1.
DR AlphaFoldDB; Q7X7L3; -.
DR SMR; Q7X7L3; -.
DR STRING; 4530.OS04T0484900-01; -.
DR PaxDb; Q7X7L3; -.
DR PRIDE; Q7X7L3; -.
DR EnsemblPlants; Os04t0484900-01; Os04t0484900-01; Os04g0484900.
DR GeneID; 4336205; -.
DR Gramene; Os04t0484900-01; Os04t0484900-01; Os04g0484900.
DR KEGG; osa:4336205; -.
DR eggNOG; KOG2535; Eukaryota.
DR HOGENOM; CLU_025983_2_1_1; -.
DR InParanoid; Q7X7L3; -.
DR OMA; TFETRPD; -.
DR OrthoDB; 320059at2759; -.
DR UniPathway; UPA00988; -.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q7X7L3; OS.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IEA:EnsemblPlants.
DR GO; GO:0033588; C:elongator holoenzyme complex; IBA:GO_Central.
DR GO; GO:0000791; C:euchromatin; IEA:EnsemblPlants.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008080; F:N-acetyltransferase activity; IEA:InterPro.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0106261; F:tRNA uridine(34) acetyltransferase activity; IEA:RHEA.
DR GO; GO:0051301; P:cell division; IEA:EnsemblPlants.
DR GO; GO:0009294; P:DNA-mediated transformation; IEA:EnsemblPlants.
DR GO; GO:0035265; P:organ growth; IEA:EnsemblPlants.
DR GO; GO:0010928; P:regulation of auxin mediated signaling pathway; IEA:EnsemblPlants.
DR GO; GO:2000025; P:regulation of leaf formation; IEA:EnsemblPlants.
DR GO; GO:0090708; P:specification of plant organ axis polarity; IEA:EnsemblPlants.
DR GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; IBA:GO_Central.
DR InterPro; IPR016181; Acyl_CoA_acyltransferase.
DR InterPro; IPR039661; ELP3.
DR InterPro; IPR034687; ELP3-like.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR000182; GNAT_dom.
DR InterPro; IPR032432; Radical_SAM_C.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR11135; PTHR11135; 1.
DR PANTHER; PTHR11135:SF7; PTHR11135:SF7; 1.
DR Pfam; PF00583; Acetyltransf_1; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF16199; Radical_SAM_C; 1.
DR PIRSF; PIRSF005669; Hist_AcTrfase_ELP3; 1.
DR SFLD; SFLDF00344; ELP3-like; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR SUPFAM; SSF55729; SSF55729; 1.
DR TIGRFAMs; TIGR01211; ELP3; 1.
DR PROSITE; PS51186; GNAT; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Acyltransferase; Iron; Iron-sulfur; Metal-binding; Nucleus;
KW Reference proteome; RNA-binding; S-adenosyl-L-methionine; Transferase;
KW tRNA processing; tRNA-binding.
FT CHAIN 1..573
FT /note="Elongator complex protein 3"
FT /id="PRO_0000232129"
FT DOMAIN 108..398
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 422..573
FT /note="N-acetyltransferase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00532"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 125
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q02908"
FT BINDING 135
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q02908"
FT BINDING 138
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q02908"
FT BINDING 190
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 500..503
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 523..525
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 556
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
SQ SEQUENCE 573 AA; 63775 MW; 9CCDB95C057F2B54 CRC64;
MATAVAAAGG GGGGEQPRRR KPAPGRGGVV LPAGLSEEEA RVRAIAEIVS AMGELSRRGE
DVDLNALKSA ACRRYGLARA PKLVEMIAAV PEADRAALLP RLRAKPVRTA SGIAVVAVMS
KPHRCPHIAT TGNICVYCPG GPDSDFEYST QSYTGYEPTS MRAIRARYNP YVQARSRIDQ
LKRLGHSVDK VEFILMGGTF MSLPADYRDY FIRNLHDALS GHTSANVEEA VCYSEHGAVK
CIGMTIETRP DYCLGPHLRQ MLSYGCTRLE IGVQSTYEDV ARDTNRGHTV AAVADCFCLA
KDAGFKVVAH MMPDLPNVGV ERDLESFREF FENPAFRADG LKIYPTLVIR GTGLYELWKT
GRYRNYPPEL LVDIVARILS MVPPWTRVYR VQRDIPMPLV TSGVEKGNLR ELALARMEDL
GLKCRDVRTR EAGIQDIHHK IRPDEVELVR RDYAANEGWE TFLSYEDTQQ DILIGLLRLR
KCGRNVTCPE LVGRCSIVRE LHVYGTAVPV HGRDADKLQH QGYGTLLMEE AERIARKEHR
SKKIAVISGV GTRHYYRKLG YELEGPYMVK CLV
