SYT_PYRAB
ID SYT_PYRAB Reviewed; 625 AA.
AC Q9UZ14; G8ZHE8;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Threonine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00184};
DE EC=6.1.1.3 {ECO:0000255|HAMAP-Rule:MF_00184};
DE AltName: Full=Threonyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00184};
DE Short=ThrRS {ECO:0000255|HAMAP-Rule:MF_00184};
GN Name=thrS {ECO:0000255|HAMAP-Rule:MF_00184}; OrderedLocusNames=PYRAB13430;
GN ORFNames=PAB1490;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
RN [3] {ECO:0007744|PDB:1Y2Q}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 1-143, DOMAIN, AND SIMILARITY
RP WITH DTD.
RX PubMed=15908961; DOI=10.1038/nsmb943;
RA Dwivedi S., Kruparani S.P., Sankaranarayanan R.;
RT "A D-amino acid editing module coupled to the translational apparatus in
RT archaea.";
RL Nat. Struct. Mol. Biol. 12:556-557(2005).
RN [4] {ECO:0007744|PDB:2HKZ, ECO:0007744|PDB:2HL0, ECO:0007744|PDB:2HL1, ECO:0007744|PDB:2HL2}
RP X-RAY CRYSTALLOGRAPHY (1.86 ANGSTROMS) OF 1-143 (EDITING DOMAIN) IN COMPLEX
RP WITH POST-TRANSFER EDITING SUBSTRATE ANALOGS, FUNCTION IN EDITING, DOMAIN,
RP AND MUTAGENESIS OF HIS-83; TYR-120; LYS-121 AND GLU-134.
RX PubMed=16902403; DOI=10.1038/sj.emboj.7601278;
RA Hussain T., Kruparani S.P., Pal B., Dock-Bregeon A.C., Dwivedi S.,
RA Shekar M.R., Sureshbabu K., Sankaranarayanan R.;
RT "Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like
RT domain in threonyl-tRNA synthetase from archaea.";
RL EMBO J. 25:4152-4162(2006).
RN [5] {ECO:0007744|PDB:3PD2, ECO:0007744|PDB:3PD3, ECO:0007744|PDB:3PD4, ECO:0007744|PDB:3PD5}
RP X-RAY CRYSTALLOGRAPHY (1.86 ANGSTROMS) OF 1-147 (EDITING DOMAIN) IN COMPLEX
RP WITH PRE- AND POST-TRANSFER EDITING SUBSTRATE ANALOGS, FUNCTION, REACTION
RP MECHANISM, AND DOMAIN.
RX PubMed=21098258; DOI=10.1073/pnas.1014299107;
RA Hussain T., Kamarthapu V., Kruparani S.P., Deshmukh M.V.,
RA Sankaranarayanan R.;
RT "Mechanistic insights into cognate substrate discrimination during
RT proofreading in translation.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:22117-22121(2010).
RN [6] {ECO:0007744|PDB:4RRQ, ECO:0007744|PDB:4RRR}
RP X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) OF 1-147 (EDITING DOMAIN) IN COMPLEX
RP WITH POST-TRANSFER EDITING SUBSTRATE ANALOGS, FUNCTION, EDITING REACTION
RP MECHANISM, DOMAIN, AND MUTAGENESIS OF HIS-83; TYR-120; LYS-121 AND GLU-134.
RX PubMed=26113036; DOI=10.1038/ncomms8552;
RA Ahmad S., Muthukumar S., Kuncha S.K., Routh S.B., Yerabham A.S.,
RA Hussain T., Kamarthapu V., Kruparani S.P., Sankaranarayanan R.;
RT "Specificity and catalysis hardwired at the RNA-protein interface in a
RT translational proofreading enzyme.";
RL Nat. Commun. 6:7552-7552(2015).
RN [7] {ECO:0007744|PDB:4S02, ECO:0007744|PDB:4S03, ECO:0007744|PDB:4S0I, ECO:0007744|PDB:4S0J, ECO:0007744|PDB:4S0K, ECO:0007744|PDB:4S0L}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 1-143.
RX PubMed=25700516; DOI=10.1126/science.aaa2424;
RA Pearson A.D., Mills J.H., Song Y., Nasertorabi F., Han G.W., Baker D.,
RA Stevens R.C., Schultz P.G.;
RT "Trapping a transition state in a computationally designed protein
RT bottle.";
RL Science 347:863-867(2015).
CC -!- FUNCTION: Catalyzes the attachment of threonine to tRNA(Thr) in a two-
CC step reaction: L-threonine is first activated by ATP to form Thr-AMP
CC and then transferred to the acceptor end of tRNA(Thr) (Probable). Edits
CC incorrectly charged L-seryl-tRNA(Thr) via its editing domain
CC (PubMed:16902403, PubMed:21098258). Deacylates correctly charged
CC glycyl-tRNA(Gly), but neither glycyl-tRNA(Gly)(2'-dA76) (the terminal
CC 2'-OH of tRNA(Thr) adenine 76 has been replaced by hydrogen) nor the
CC 2'-fluoro tRNA derivative do so, strongly suggesting the editing
CC function is tRNA catalyzed (PubMed:26113036).
CC {ECO:0000269|PubMed:16902403, ECO:0000269|PubMed:21098258,
CC ECO:0000269|PubMed:26113036}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-
CC threonyl-tRNA(Thr); Xref=Rhea:RHEA:24624, Rhea:RHEA-COMP:9670,
CC Rhea:RHEA-COMP:9704, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57926, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78534, ChEBI:CHEBI:456215; EC=6.1.1.3;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00184};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00184};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00184};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00184}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00184}.
CC -!- DOMAIN: The N-terminal domain (about residues 1-143) is an archaea-
CC specific tRNA-editing domain (PubMed:16902403) that has a highly
CC similar structure to Dtd (D-aminoacyl-tRNA deacylase); the domain binds
CC L-serine and L-cysteine and most D-amino acids but not L-threonine
CC (PubMed:15908961, PubMed:16902403). Editing of incorrectly charged L-
CC seryl-tRNA(Thr) by this domain is tRNA catalyzed (PubMed:16902403,
CC PubMed:21098258, PubMed:26113036). {ECO:0000269|PubMed:15908961,
CC ECO:0000269|PubMed:16902403, ECO:0000269|PubMed:21098258,
CC ECO:0000269|PubMed:26113036}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_00184}.
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DR EMBL; AJ248287; CAB50248.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70785.1; -; Genomic_DNA.
DR PIR; C75044; C75044.
DR RefSeq; WP_010868458.1; NC_000868.1.
DR PDB; 1Y2Q; X-ray; 1.95 A; A=1-143.
DR PDB; 2HKZ; X-ray; 2.10 A; A=1-143.
DR PDB; 2HL0; X-ray; 1.86 A; A=1-143.
DR PDB; 2HL1; X-ray; 2.25 A; A/B=1-147.
DR PDB; 2HL2; X-ray; 2.60 A; A/B=1-143.
DR PDB; 3PD2; X-ray; 1.86 A; A/B=1-147.
DR PDB; 3PD3; X-ray; 1.86 A; A/B=1-147.
DR PDB; 3PD4; X-ray; 2.40 A; A/B=1-147.
DR PDB; 3PD5; X-ray; 2.29 A; A/B=1-147.
DR PDB; 4RRQ; X-ray; 1.79 A; A/B=1-147.
DR PDB; 4RRR; X-ray; 1.86 A; A/B=1-147.
DR PDB; 4S02; X-ray; 1.95 A; A=1-143.
DR PDB; 4S03; X-ray; 2.05 A; A=1-143.
DR PDB; 4S0I; X-ray; 2.36 A; A=1-143.
DR PDB; 4S0J; X-ray; 2.10 A; A=1-143.
DR PDB; 4S0K; X-ray; 2.10 A; A=1-143.
DR PDB; 4S0L; X-ray; 2.50 A; A=1-143.
DR PDBsum; 1Y2Q; -.
DR PDBsum; 2HKZ; -.
DR PDBsum; 2HL0; -.
DR PDBsum; 2HL1; -.
DR PDBsum; 2HL2; -.
DR PDBsum; 3PD2; -.
DR PDBsum; 3PD3; -.
DR PDBsum; 3PD4; -.
DR PDBsum; 3PD5; -.
DR PDBsum; 4RRQ; -.
DR PDBsum; 4RRR; -.
DR PDBsum; 4S02; -.
DR PDBsum; 4S03; -.
DR PDBsum; 4S0I; -.
DR PDBsum; 4S0J; -.
DR PDBsum; 4S0K; -.
DR PDBsum; 4S0L; -.
DR AlphaFoldDB; Q9UZ14; -.
DR SMR; Q9UZ14; -.
DR STRING; 272844.PAB1490; -.
DR EnsemblBacteria; CAB50248; CAB50248; PAB1490.
DR GeneID; 1496731; -.
DR KEGG; pab:PAB1490; -.
DR PATRIC; fig|272844.11.peg.1427; -.
DR eggNOG; arCOG00401; Archaea.
DR HOGENOM; CLU_029833_0_0_2; -.
DR OMA; DAHIFML; -.
DR OrthoDB; 11656at2157; -.
DR PhylomeDB; Q9UZ14; -.
DR BRENDA; 6.1.1.3; 5242.
DR EvolutionaryTrace; Q9UZ14; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IEA:UniProt.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004829; F:threonine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006435; P:threonyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00771; ThrRS_core; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR Gene3D; 3.40.50.800; -; 1.
DR Gene3D; 3.50.80.10; -; 1.
DR HAMAP; MF_00184; Thr_tRNA_synth; 1.
DR InterPro; IPR002314; aa-tRNA-synt_IIb.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004154; Anticodon-bd.
DR InterPro; IPR036621; Anticodon-bd_dom_sf.
DR InterPro; IPR023509; DTD-like_sf.
DR InterPro; IPR002320; Thr-tRNA-ligase_IIa.
DR InterPro; IPR015011; Threonyl-tRNA_syn_edit_dom_arc.
DR InterPro; IPR033728; ThrRS_core.
DR PANTHER; PTHR11451; PTHR11451; 1.
DR Pfam; PF03129; HGTP_anticodon; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR Pfam; PF08915; tRNA-Thr_ED; 1.
DR PRINTS; PR01047; TRNASYNTHTHR.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00418; thrS; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Metal-binding; Nucleotide-binding; Protein biosynthesis; RNA-binding;
KW tRNA-binding; Zinc.
FT CHAIN 1..625
FT /note="Threonine--tRNA ligase"
FT /id="PRO_0000101107"
FT REGION 1..143
FT /note="Editing domain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00184,
FT ECO:0000305|PubMed:15908961, ECO:0000305|PubMed:16902403,
FT ECO:0000305|PubMed:21098258, ECO:0000305|PubMed:26113036"
FT REGION 206..505
FT /note="Catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00184"
FT BINDING 298
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00184"
FT BINDING 350
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00184"
FT BINDING 474
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00184"
FT MUTAGEN 83
FT /note="H->A: Isolated domain has decreased to no
FT deacylation of mischarged L-seryl-tRNA(Thr). Deacylates
FT correctly charged glycyl-tRNA(Gly)."
FT /evidence="ECO:0000269|PubMed:16902403,
FT ECO:0000269|PubMed:26113036"
FT MUTAGEN 120
FT /note="Y->A: Isolated domain has nearly wild-type
FT deacylation of mischarged L-seryl-tRNA(Thr), no longer
FT binds L-Ser or L-Cys. No activity on threonyl-tRNA(Thr).
FT Same results; when associated with A-134."
FT /evidence="ECO:0000269|PubMed:16902403,
FT ECO:0000269|PubMed:26113036"
FT MUTAGEN 121
FT /note="K->M: Isolated domain has nearly wild-type
FT deacylation of mischarged L-seryl-tRNA(Thr). Later shown
FT not to deacylate L-seryl-tRNA(Thr), no activity on L-
FT threonyl-tRNA(Thr)."
FT /evidence="ECO:0000269|PubMed:16902403,
FT ECO:0000269|PubMed:26113036"
FT MUTAGEN 121
FT /note="K->S: Isolated domain does not deacylate mischarged
FT L-seryl-tRNA(Thr)."
FT /evidence="ECO:0000269|PubMed:16902403"
FT MUTAGEN 134
FT /note="E->A: Isolated domain has nearly wild-type
FT deacylation of mischarged L-seryl-tRNA(Thr). No activity on
FT L-threonyl-tRNA(Thr). Same results; when associated with A-
FT 120."
FT /evidence="ECO:0000269|PubMed:16902403,
FT ECO:0000269|PubMed:26113036"
FT STRAND 2..22
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 28..31
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 32..44
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 47..51
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 53..71
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 75..80
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 91..107
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 117..127
FT /evidence="ECO:0007829|PDB:4RRQ"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:4RRQ"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:3PD2"
SQ SEQUENCE 625 AA; 73372 MW; AF8E48AAE789124F CRC64;
MRVLLIHSDY IEYEVKDKAL KNPEPISEDM KRGRMEEVLV AFISVEKVDE KNPEEVSLKA
IEEISKVAEQ VKAENVFVYP FAHLSSELAK PSVAMDILNR VYQGLKERGF NVGKAPFGYY
KAFKISCKGH PLAELSRTIV PEEARVEEVP EALRKEEEEL VSYWYILTPE GELIEVDKFD
FTGYENLRKF VNYEIAKNRI AEKEPPHVKL MLEHELVDYE PGSDPGNLRY YPKGRLIKSL
LEQYVTEKVI EYGAMEVETP IMYDFEHPAL EKYLNRFPAR QYIVLSGDKR YFLRFAACFG
QFMIKKDAII SYRNLPLRMY ELTRYSFRRE KRGELSGLRR LRAFTMPDMH TLAKDIEQAK
EEFKKQFKLS MEVLEGVGLT PEDYEVAIRF TEDFWKEHKD FIVELVKLIG KPVLIEMWKQ
RFFYFILKFE FNFVDNLDKA AALSTVQIDV ENAERFGITY YDENGEEKYP LILHCSPSGA
IERVMYAILE KQAKLMNEGK KPMFPLWLSP IQVRVIPVSE EYLDYALYVA GKLEGAKIRV
DVDDEDERLN KKIRRAEKEW IPYIVVVGAR EKENGTITVR RREDGKQYET RIEELIKEIK
EKTEGFPYKP RPLPLLLSKR PKFRG
