ELP3_DEHMC
ID ELP3_DEHMC Reviewed; 459 AA.
AC A0A1C7D1B7;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 18-SEP-2019, sequence version 2.
DT 03-AUG-2022, entry version 26.
DE RecName: Full=tRNA uridine(34) acetyltransferase {ECO:0000305};
DE EC=2.3.1.- {ECO:0000269|PubMed:27455459};
DE AltName: Full=Elongator complex protein 3 homolog {ECO:0000303|PubMed:30733442};
DE Short=DmcElp3 {ECO:0000303|PubMed:27455459, ECO:0000303|PubMed:30733442};
GN ORFNames=cbdbA595;
OS Dehalococcoides mccartyi (strain CBDB1).
OC Bacteria; Chloroflexi; Dehalococcoidia; Dehalococcoidales;
OC Dehalococcoidaceae; Dehalococcoides.
OX NCBI_TaxID=255470;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CBDB1;
RX PubMed=16116419; DOI=10.1038/nbt1131;
RA Kube M., Beck A., Zinder S.H., Kuhl H., Reinhardt R., Adrian L.;
RT "Genome sequence of the chlorinated compound-respiring bacterium
RT Dehalococcoides species strain CBDB1.";
RL Nat. Biotechnol. 23:1269-1273(2005).
RN [2] {ECO:0000312|PDB:5L7L}
RP X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR AND
RP ZINC, FUNCTION, CATALYTIC ACTIVITY, PATHWAY, COFACTOR, SUBUNIT, AND
RP MUTAGENESIS OF LYS-2; LYS-3; ARG-6; 27-CYS--CYS-30; HIS-73; LYS-77;
RP ARG-155; LYS-193; LYS-229; ARG-274; ARG-277; ARG-280 AND ARG-314.
RX PubMed=27455459; DOI=10.1038/nsmb.3265;
RA Glatt S., Zabel R., Kolaj-Robin O., Onuma O.F., Baudin F., Graziadei A.,
RA Taverniti V., Lin T.Y., Baymann F., Seraphin B., Breunig K.D.,
RA Mueller C.W.;
RT "Structural basis for tRNA modification by Elp3 from Dehalococcoides
RT mccartyi.";
RL Nat. Struct. Mol. Biol. 23:794-802(2016).
RN [3] {ECO:0007744|PDB:6IA6}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 2-446 IN COMPLEX WITH ACETYL-COA
RP AND IRON-SULFUR.
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:27455459). The proposed mechanism is the following: (i)
CC recruits S-adenosyl-L-methionine and cleaves it to generate a 5'-
CC deoxyadenosine radical (5'-dA) in the radical S-adenosyl-L-methionine
CC (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-acetyltransferase
CC domain and (iii) an acetyl radical is formed by the products of the two
CC domains and (iv) is transferred onto the C5 position of uridine(34) in
CC the bound tRNA molecule. Does not show protein lysine acetyltransferase
CC activity (By similarity). {ECO:0000250|UniProtKB:D5VRB9,
CC ECO:0000269|PubMed:27455459}.
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:27455459};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61021;
CC Evidence={ECO:0000269|PubMed:27455459};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:27455459};
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:27455459}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:27455459}.
CC -!- SIMILARITY: Belongs to the ELP3 family. {ECO:0000305}.
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DR EMBL; AJ965256; CAI82774.1; -; Genomic_DNA.
DR RefSeq; WP_011309125.1; NC_007356.1.
DR PDB; 5L7L; X-ray; 2.59 A; A=1-459.
DR PDB; 6IA6; X-ray; 2.70 A; A=2-459.
DR PDBsum; 5L7L; -.
DR PDBsum; 6IA6; -.
DR AlphaFoldDB; A0A1C7D1B7; -.
DR SMR; A0A1C7D1B7; -.
DR KEGG; deh:cbdbA595; -.
DR OMA; TFETRPD; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IDA:UniProtKB.
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; ISS:UniProtKB.
DR GO; GO:0051391; P:tRNA acetylation; IDA:UniProtKB.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IDA:UniProtKB.
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: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; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Acyltransferase; Iron; Iron-sulfur; Metal-binding;
KW RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing;
KW tRNA-binding; Zinc.
FT CHAIN 1..459
FT /note="tRNA uridine(34) acetyltransferase"
FT /id="PRO_0000447990"
FT DOMAIN 6..271
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 1..278
FT /note="Radical S-adenosyl-L-methionine (rSAM)"
FT /evidence="ECO:0000303|PubMed:27455459"
FT REGION 308..459
FT /note="N-acetyltransferase"
FT /evidence="ECO:0000303|PubMed:27455459"
FT BINDING 23
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 27
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:27455459,
FT ECO:0000269|PubMed:30733442, ECO:0007744|PDB:5L7L,
FT ECO:0007744|PDB:6IA6"
FT BINDING 30
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:27455459,
FT ECO:0000269|PubMed:30733442, ECO:0007744|PDB:5L7L,
FT ECO:0007744|PDB:6IA6"
FT BINDING 77
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000269|PubMed:30733442,
FT ECO:0007744|PDB:6IA6"
FT BINDING 310
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27455459,
FT ECO:0007744|PDB:5L7L"
FT BINDING 312
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27455459,
FT ECO:0007744|PDB:5L7L"
FT BINDING 315
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27455459,
FT ECO:0007744|PDB:5L7L"
FT BINDING 386..389
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000269|PubMed:30733442,
FT ECO:0007744|PDB:6IA6"
FT BINDING 409..411
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000269|PubMed:30733442,
FT ECO:0007744|PDB:6IA6"
FT BINDING 442
FT /ligand="acetyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57288"
FT /evidence="ECO:0000269|PubMed:30733442,
FT ECO:0007744|PDB:6IA6"
FT MUTAGEN 2
FT /note="K->A: Abolished tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 3
FT /note="K->A: Abolished tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 6
FT /note="R->A: Abolished tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 27..30
FT /note="CIYC->SIYS: Does not abolishes homodimerization."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 73
FT /note="H->A: Slightly reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 77
FT /note="K->A: Slightly reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 155
FT /note="R->A: Slightly reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 193
FT /note="K->A: Slightly reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 229
FT /note="K->A: Reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 274
FT /note="R->A: Reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 277
FT /note="R->A: Reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 280
FT /note="R->A: Reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT MUTAGEN 314
FT /note="R->A: Reduced tRNA-binding."
FT /evidence="ECO:0000269|PubMed:27455459"
FT STRAND 12..17
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:6IA6"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 45..52
FT /evidence="ECO:0007829|PDB:5L7L"
FT TURN 53..55
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 57..71
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 76..85
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 92..107
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 114..121
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 124..135
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 142..151
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 155..163
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 170..173
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 177..189
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 193..198
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 207..216
FT /evidence="ECO:0007829|PDB:5L7L"
FT TURN 217..219
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 226..230
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:6IA6"
FT HELIX 240..246
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 255..266
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 274..277
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 332..340
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 343..351
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 357..365
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 375..377
FT /evidence="ECO:0007829|PDB:6IA6"
FT STRAND 381..389
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 408..423
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 428..432
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 436..438
FT /evidence="ECO:0007829|PDB:5L7L"
FT HELIX 439..443
FT /evidence="ECO:0007829|PDB:5L7L"
FT TURN 444..446
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 448..450
FT /evidence="ECO:0007829|PDB:5L7L"
FT STRAND 453..457
FT /evidence="ECO:0007829|PDB:5L7L"
SQ SEQUENCE 459 AA; 51188 MW; 502885206EA39009 CRC64;
MKKLSRTISG VTPVAVMTKP LPCPGKCIYC PTFAATPQSY TPESPAVLRA KSCEYQAYKQ
VALRLRIIQD MGHPTDKVEL IIMGGTFLSA DITYQYGFIK DCYDALNGVV AGSLEEAKTI
NETAQHRCVG LCIETRPDIC GKAEIQRMID FGTTRVELGV QMLDDDIYKL VERGHRVSDV
AEATCLLREY GLKVHYHWMP GLPGSSPEKD LALSRMVFED PRFCPDGLKL YPTMVVEGTI
LEQWWKEGRY TPYPNGTMTG LIADIKALVP PYVRISRVLR DIPAVFISAG LKDSLRDGVR
QILESRHQKC RCIRCREYGH RQRKGQTSGE PTLRRLDYPA SGGKEIFLSF EDASDTLYGL
LRLRIPCASL PVLGQKYGAK TGLVRELHVY GTELSLGEQG DQSAQHRGLG RKLLAEAECL
ARDEFGLDSL AILSGVGARE YYRSLGYELV AGYMCKHLD
