TTUA_PYRHO
ID TTUA_PYRHO Reviewed; 310 AA.
AC O58038;
DT 22-NOV-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=tRNA-5-methyluridine(54) 2-sulfurtransferase {ECO:0000305|PubMed:28655838};
DE EC=2.8.1.- {ECO:0000269|PubMed:28655838};
DE AltName: Full=tRNA thiouridine synthetase TtuA {ECO:0000303|PubMed:23444054};
GN Name=ttuA {ECO:0000303|PubMed:23444054, ECO:0000303|PubMed:28655838};
GN OrderedLocusNames=PH0300 {ECO:0000312|EMBL:BAA29373.1};
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2] {ECO:0007744|PDB:3VRH}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH ZINC, DISULFIDE
RP BOND, SUBUNIT, ATP-BINDING, AND MUTAGENESIS OF ASP-59.
RX PubMed=23444054; DOI=10.1002/prot.24273;
RA Nakagawa H., Kuratani M., Goto-Ito S., Ito T., Katsura K., Terada T.,
RA Shirouzu M., Sekine S., Shigi N., Yokoyama S.;
RT "Crystallographic and mutational studies on the tRNA thiouridine synthetase
RT TtuA.";
RL Proteins 81:1232-1244(2013).
RN [3] {ECO:0007744|PDB:5MKO, ECO:0007744|PDB:5MKP, ECO:0007744|PDB:5MKQ}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEXES WITH AMP; ZINC AND
RP 4FE-4S CLUSTER, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, DISULFIDE
RP BOND, REACTION MECHANISM, AND PATHWAY.
RX PubMed=28655838; DOI=10.1073/pnas.1700902114;
RA Arragain S., Bimai O., Legrand P., Caillat S., Ravanat J.L., Touati N.,
RA Binet L., Atta M., Fontecave M., Golinelli-Pimpaneau B.;
RT "Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S]
RT cluster.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:7355-7360(2017).
CC -!- FUNCTION: Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine
CC residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-
CC thiouridine (m(5)s(2)U or s(2)T) (PubMed:28655838). This modification
CC allows thermal stabilization of tRNAs in thermophilic microorganisms,
CC and is required for cell growth at high temperatures (By similarity).
CC Can use free sulfide as sulfur source in vitro, which may be also the
CC sulfur source in vivo (PubMed:28655838). {ECO:0000250|UniProtKB:Q72LF3,
CC ECO:0000269|PubMed:28655838}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methyluridine(54) in tRNA + ATP + hydrogen sulfide = 5-
CC methyl-2-thiouridine(54) in tRNA + AMP + diphosphate;
CC Xref=Rhea:RHEA:55188, Rhea:RHEA-COMP:10167, Rhea:RHEA-COMP:13344,
CC ChEBI:CHEBI:29919, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:74447, ChEBI:CHEBI:136799, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:28655838};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:28655838};
CC Note=Binds 1 [4Fe-4S] cluster per subunit. The cluster is chelated by
CC three Cys residues, the fourth Fe with a free coordination site may
CC bind a small ligand, such as exogenous sulfide, thus acting as a sulfur
CC carrier. {ECO:0000269|PubMed:28655838};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:28655838};
CC -!- PATHWAY: tRNA modification. {ECO:0000269|PubMed:28655838}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23444054,
CC ECO:0000269|PubMed:28655838}.
CC -!- MISCELLANEOUS: In TtuA from T.thermophilus, the sulfur inserted into
CC the nucleoside comes from the C-terminal thiocarboxylate of TtuB, but
CC there is no TtuB ortholog in P.horikoshii. Free sulfide has been shown
CC to be present at relatively high concentrations within thermophilic
CC archaea, and may be the sulfur source in vivo. {ECO:0000305}.
CC -!- MISCELLANEOUS: The thiolation reaction likely consists of two steps: a
CC first activation step by ATP to form an adenylated intermediate of the
CC target base of tRNA, and a second nucleophilic substitution step of the
CC sulfur (S) atom supplied by the hydrosulfide attached to the Fe-S
CC cluster. {ECO:0000305|PubMed:28655838}.
CC -!- SIMILARITY: Belongs to the TtcA family. TtuA subfamily. {ECO:0000305}.
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DR EMBL; BA000001; BAA29373.1; -; Genomic_DNA.
DR PIR; F71455; F71455.
DR RefSeq; WP_010884395.1; NC_000961.1.
DR PDB; 3VRH; X-ray; 2.10 A; A=1-310.
DR PDB; 5MKO; X-ray; 2.65 A; A/B=1-310.
DR PDB; 5MKP; X-ray; 2.50 A; A=1-310.
DR PDB; 5MKQ; X-ray; 2.79 A; A/B=1-310.
DR PDBsum; 3VRH; -.
DR PDBsum; 5MKO; -.
DR PDBsum; 5MKP; -.
DR PDBsum; 5MKQ; -.
DR AlphaFoldDB; O58038; -.
DR SMR; O58038; -.
DR STRING; 70601.3256690; -.
DR EnsemblBacteria; BAA29373; BAA29373; BAA29373.
DR GeneID; 1444182; -.
DR KEGG; pho:PH0300; -.
DR eggNOG; arCOG00042; Archaea.
DR OMA; CLHINLG; -.
DR OrthoDB; 57500at2157; -.
DR BRENDA; 2.8.1.15; 5244.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0034227; P:tRNA thio-modification; IEA:InterPro.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IEA:InterPro.
DR Gene3D; 3.40.50.620; -; 1.
DR InterPro; IPR000541; Ncs6/Tuc1/Ctu1.
DR InterPro; IPR001763; Rhodanese-like_dom.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR011063; TilS/TtcA_N.
DR InterPro; IPR035107; tRNA_thiolation_TtcA_Ctu1.
DR Pfam; PF01171; ATP_bind_3; 1.
DR PIRSF; PIRSF004976; ATPase_YdaO; 1.
DR TIGRFAMs; TIGR00269; TIGR00269; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; ATP-binding; Disulfide bond; Iron; Iron-sulfur;
KW Magnesium; Metal-binding; Nucleotide-binding; RNA-binding; Transferase;
KW tRNA processing; tRNA-binding; Zinc.
FT CHAIN 1..310
FT /note="tRNA-5-methyluridine(54) 2-sulfurtransferase"
FT /id="PRO_0000442361"
FT BINDING 3
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 6
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 22
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 25
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 79
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 128
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 131
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 135
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 154
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 220
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:28655838"
FT BINDING 272
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 275
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 284
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT BINDING 287
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT DISULFID 128..220
FT /note="Alternate"
FT /evidence="ECO:0000269|PubMed:23444054,
FT ECO:0000269|PubMed:28655838, ECO:0007744|PDB:3VRH"
FT MUTAGEN 59
FT /note="D->A: Loss of binding to ATP."
FT /evidence="ECO:0000269|PubMed:23444054"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:3VRH"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 23..40
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 58..69
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:3VRH"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 87..101
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 105..109
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 110..114
FT /evidence="ECO:0007829|PDB:3VRH"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:5MKO"
FT HELIX 127..145
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 157..169
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 180..183
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:3VRH"
FT TURN 195..198
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 201..211
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 228..241
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 245..256
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:5MKO"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 280..283
FT /evidence="ECO:0007829|PDB:3VRH"
FT HELIX 285..290
FT /evidence="ECO:0007829|PDB:3VRH"
FT STRAND 304..306
FT /evidence="ECO:0007829|PDB:5MKQ"
SQ SEQUENCE 310 AA; 35633 MW; 87870CE4006C4246 CRC64;
MKCKFCSREA YIKIHYPKMY LCEEHFKEYF ERKVSRTIER YKLLTKDERI LVAVSGGKDS
AVTAYVLKKL GYNIECLHIN LGISGYSEKS EEYAKKQCKL IGAPLHIVRI KEILGYGIGE
VKTRRPPCSY CGLTKRYIMN KFAYDNGFDA IATGHNLDDE ASFLLNNILH WNTEYLAKGG
PILPQQGKFI KKVKPLYEVT EREVVAYALA VGLEYIVEEC PYARGATTLD MKGVLNELEE
KRPGTKFNFV RGYLKKKKLF EPEIKEKEIK ECKICRMPSS GDICAFCKFW GLKKEINFKV
SSTDEEPFGP
