ELP3_METIM
ID ELP3_METIM Reviewed; 534 AA.
AC D5VRB9;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=tRNA uridine(34) acetyltransferase {ECO:0000305};
DE EC=2.3.1.- {ECO:0000269|PubMed:25151136};
DE AltName: Full=Elongator complex protein 3 homolog {ECO:0000303|PubMed:30733442};
DE Short=MinElp3 {ECO:0000303|PubMed:30733442};
GN OrderedLocusNames=Metin_0452 {ECO:0000312|EMBL:ADG13122.1};
OS Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=573063;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11812 / JCM 15783 / ME;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Munk A.C., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA Kyrpides N., Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Woyke T.;
RT "Complete sequence of Methanocaldococcus infernus ME.";
RL Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND MUTAGENESIS OF 95-CYS--CYS-98
RP AND TYR-517.
RX PubMed=25151136; DOI=10.1038/nchembio.1610;
RA Selvadurai K., Wang P., Seimetz J., Huang R.H.;
RT "Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a
RT radical mechanism.";
RL Nat. Chem. Biol. 10:810-812(2014).
RN [3] {ECO:0007744|PDB:6IA8, ECO:0007744|PDB:6IAD, ECO:0007744|PDB:6IAZ}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 47-534, FUNCTION, PATHWAY,
RP DISULFIDE BONDS, AND MUTAGENESIS OF LYS-150; LYS-266; GLN-461; HIS-463 AND
RP TYR-517.
RX PubMed=30733442; DOI=10.1038/s41467-019-08579-2;
RA Lin T.Y., Abbassi N.E.H., Zakrzewski K., Chramiec-Glabik A.,
RA Jemiola-Rzeminska M., Rozycki J., Glatt S.;
RT "The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.";
RL Nat. Commun. 10:625-625(2019).
CC -!- FUNCTION: tRNA uridine(34) acetyltransferase, which mediates formation
CC of carboxymethyluridine in the wobble base at position 34 in tRNAs
CC (PubMed:25151136, PubMed:30733442). The proposed mechanism is the
CC following: (i) recruits S-adenosyl-L-methionine and cleaves it to
CC generate a 5'-deoxyadenosine radical (5'-dA) in the radical S-adenosyl-
CC L-methionine (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-
CC acetyltransferase domain and (iii) an acetyl radical is formed by the
CC products of the two domains and (iv) is transferred onto the C5
CC position of uridine(34) in the bound tRNA molecule (PubMed:25151136).
CC Does not show protein lysine acetyltransferase activity
CC (PubMed:30733442). {ECO:0000269|PubMed:25151136,
CC ECO:0000269|PubMed:30733442}.
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:0000269|PubMed:25151136};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61021;
CC Evidence={ECO:0000269|PubMed:25151136};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
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. {ECO:0000269|PubMed:25151136,
CC ECO:0000269|PubMed:30733442}.
CC -!- SIMILARITY: Belongs to the ELP3 family. {ECO:0000305}.
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DR EMBL; CP002009; ADG13122.1; -; Genomic_DNA.
DR RefSeq; WP_013099868.1; NC_014122.1.
DR PDB; 6IA8; X-ray; 1.90 A; A=21-534.
DR PDB; 6IAD; X-ray; 2.05 A; A=55-534.
DR PDB; 6IAZ; X-ray; 1.90 A; A=47-534.
DR PDBsum; 6IA8; -.
DR PDBsum; 6IAD; -.
DR PDBsum; 6IAZ; -.
DR AlphaFoldDB; D5VRB9; -.
DR SMR; D5VRB9; -.
DR STRING; 573063.Metin_0452; -.
DR EnsemblBacteria; ADG13122; ADG13122; Metin_0452.
DR GeneID; 9131457; -.
DR KEGG; mif:Metin_0452; -.
DR eggNOG; arCOG01361; Archaea.
DR HOGENOM; CLU_025983_2_1_2; -.
DR OMA; TFETRPD; -.
DR OrthoDB; 7724at2157; -.
DR Proteomes; UP000002061; Chromosome.
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:1904047; F:S-adenosyl-L-methionine binding; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0106261; F:tRNA uridine(34) acetyltransferase activity; IDA:UniProtKB.
DR GO; GO:0051391; P:tRNA acetylation; IDA:UniProtKB.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IDA:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR016181; Acyl_CoA_acyltransferase.
DR InterPro; IPR013785; Aldolase_TIM.
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:SF0; PTHR11135:SF0; 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 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Acyltransferase; Disulfide bond; Iron; Iron-sulfur;
KW Metal-binding; RNA-binding; S-adenosyl-L-methionine; Transferase;
KW tRNA processing; tRNA-binding.
FT CHAIN 1..534
FT /note="tRNA uridine(34) acetyltransferase"
FT /id="PRO_0000447989"
FT DOMAIN 73..344
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 387..534
FT /note="N-acetyltransferase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00532"
FT REGION 70..330
FT /note="Radical S-adenosyl-L-methionine (rSAM)"
FT /evidence="ECO:0000303|PubMed:25151136"
FT BINDING 90
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 95
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 98
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 150
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 461..464
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 485..487
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT BINDING 518
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000250|UniProtKB:A0A1C7D1B7"
FT DISULFID 384..389
FT /evidence="ECO:0000269|PubMed:30733442,
FT ECO:0007744|PDB:6IA8, ECO:0007744|PDB:6IAD,
FT ECO:0007744|PDB:6IAZ"
FT MUTAGEN 95..98
FT /note="CIFC->SIFS: Abolished tRNA uridine(34)
FT acetyltransferase activity."
FT /evidence="ECO:0000269|PubMed:25151136"
FT MUTAGEN 150
FT /note="K->A: Strongly reduced tRNA acetyl-coA hydrolase
FT activity."
FT /evidence="ECO:0000269|PubMed:30733442"
FT MUTAGEN 266
FT /note="K->A: Strongly reduced tRNA acetyl-coA hydrolase
FT activity."
FT /evidence="ECO:0000269|PubMed:30733442"
FT MUTAGEN 461
FT /note="Q->A: Strongly reduced tRNA acetyl-coA hydrolase
FT activity."
FT /evidence="ECO:0000269|PubMed:30733442"
FT MUTAGEN 463
FT /note="H->A: Does not affect tRNA acetyl-coA hydrolase
FT activity."
FT /evidence="ECO:0000269|PubMed:30733442"
FT MUTAGEN 517
FT /note="Y->A: Abolished tRNA uridine(34) acetyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:25151136,
FT ECO:0000269|PubMed:30733442"
FT STRAND 75..84
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 130..143
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 149..158
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 165..180
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 187..194
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 197..208
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 215..224
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 228..234
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 238..243
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 250..261
FT /evidence="ECO:0007829|PDB:6IA8"
FT TURN 262..264
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 266..271
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 280..292
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 299..303
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 313..319
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 328..341
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 357..359
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 360..363
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 369..380
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 387..390
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 392..399
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 405..407
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 408..417
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 420..429
FT /evidence="ECO:0007829|PDB:6IA8"
FT TURN 430..433
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 434..443
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 456..464
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 468..470
FT /evidence="ECO:0007829|PDB:6IAD"
FT STRAND 473..475
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 481..484
FT /evidence="ECO:0007829|PDB:6IAD"
FT HELIX 485..499
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 504..508
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 512..514
FT /evidence="ECO:0007829|PDB:6IA8"
FT HELIX 515..520
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 524..526
FT /evidence="ECO:0007829|PDB:6IA8"
FT STRAND 529..533
FT /evidence="ECO:0007829|PDB:6IA8"
SQ SEQUENCE 534 AA; 61939 MW; 02FF1FCA2BCBAE1A CRC64;
MKEKLMRCII ERILKEYKEG KTLDKKRIEQ IKSECLRIYR IGIGHPSNSE ILKYATEEEK
KILIPILRKK PVRTISGVAV VAVMTSPAKC PHGKCIFCPG GLDSVFGDVP QSYTGREPAT
MRGLMFNFDP YLQTRARIEQ LEKVGHPTDK IELIIMGGTF PAREIEYQDW FIKRCLDAMN
ERESKSLEEA QKINETAKHR CVALCIETRP DYCSEKEINQ MLKLGATRVE LGVQSIYNEI
LKLCKRGHSV EDTIKATQLL KDSGLKVSYH LMPGMPGSSI EMDKKMFKEI FTNPDFMPDM
VKIYPCLVIE GTELYEMWKR GEFKPYREEE AIEVISYAKS IMPKWVRTSR IQRDIPATVI
VDGVKKSNLG ELVYKYMEKK GLRCRCIRCR EVGHVYYKKG ILPDPEHIKL VREDYEASGG
TEIFLSFEDV KNDILIAFLR LRDPYKPFRK EIDDKTMLVR QLHVFGWEKA LTRDIKEVSW
QHMGYGRMLM KEAERIAKEE FGKKKILVTS GIGVREYYRK LGYKRVGAYM GKEL
