SYTE_AERPE
ID SYTE_AERPE Reviewed; 421 AA.
AC Q9YFY3;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 26-JUN-2007, sequence version 2.
DT 25-MAY-2022, entry version 108.
DE RecName: Full=Threonine--tRNA ligase editing subunit {ECO:0000305};
DE AltName: Full=Ser-tRNA(Thr) hydrolase {ECO:0000305};
DE AltName: Full=Threonyl-tRNA synthetase 2;
DE Short=ThrRS 2 {ECO:0000303|PubMed:26113036};
DE AltName: Full=Threonyl-tRNA synthetase editing subunit {ECO:0000305};
DE Short=ThrS-ed {ECO:0000305};
GN Name=thrS2; OrderedLocusNames=APE_0117.1;
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
RN [2] {ECO:0007744|PDB:4RR6, ECO:0007744|PDB:4RR8, ECO:0007744|PDB:4RRA, ECO:0007744|PDB:4RRC, ECO:0007744|PDB:4RRD, ECO:0007744|PDB:4RRH, ECO:0007744|PDB:4RRI, ECO:0007744|PDB:4RRJ, ECO:0007744|PDB:4RRK, ECO:0007744|PDB:4RRL, ECO:0007744|PDB:4RRM}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 1-136 (WILD-TYPE AND MUTANT
RP EDITING DOMAIN) IN COMPLEX WITH POST-TRANSFER EDITING SUBSTRATE ANALOGS,
RP FUNCTION, EDITING REACTION MECHANISM, DOMAIN, AND MUTAGENESIS OF HIS-77;
RP TYR-115 AND GLU-129.
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).
CC -!- FUNCTION: Freestanding tRNA editing subunit of threonine--tRNA ligase,
CC the catalytic subunit is probably AC Q9YDW0. Deacylates (edits)
CC mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly
CC charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not
CC aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged
CC glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH
CC of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA
CC derivative, strongly suggesting the editing function is catalyzed by
CC the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).
CC {ECO:0000250|UniProtKB:Q980D1, ECO:0000269|PubMed:26113036}.
CC -!- SUBUNIT: Probably interacts with its catalytic subunit (By similarity).
CC {ECO:0000250|UniProtKB:Q980D1}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: The N-terminal domain (about residues 1-140) is an archaea-
CC specific tRNA-editing domain (PubMed:26113036) that has a highly
CC similar structure to Dtd (D-aminoacyl-tRNA deacylase). Editing of
CC incorrectly charged L-seryl-tRNA(Thr) by this domain is tRNA catalyzed
CC (PubMed:26113036). {ECO:0000269|PubMed:26113036}.
CC -!- MISCELLANEOUS: There are two ThrRS in this archaeon. The first one
CC (APE_0809.1, AC Q9YDW0) is most similar to bacterial ThrRS but it lacks
CC the N-terminal editing domain. The second one (APE_0117.1, this entry)
CC is most similar to archaeal ThrRS but lacks the central catalytic
CC domain; it probably does not aminoacylate tRNA(Thr). {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Archaea-specific ThrRS editing domain subfamily. {ECO:0000305}.
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DR EMBL; BA000002; BAA79028.2; -; Genomic_DNA.
DR PIR; B72766; B72766.
DR PDB; 4RR6; X-ray; 1.88 A; A=1-136.
DR PDB; 4RR7; X-ray; 1.86 A; A=1-136.
DR PDB; 4RR8; X-ray; 1.86 A; A=1-136.
DR PDB; 4RR9; X-ray; 1.67 A; A=1-136.
DR PDB; 4RRA; X-ray; 1.70 A; A=1-136.
DR PDB; 4RRB; X-ray; 2.10 A; A=1-136.
DR PDB; 4RRC; X-ray; 1.86 A; A=1-136.
DR PDB; 4RRD; X-ray; 1.86 A; A=1-136.
DR PDB; 4RRH; X-ray; 1.55 A; A=1-136.
DR PDB; 4RRI; X-ray; 1.50 A; A=1-136.
DR PDB; 4RRJ; X-ray; 1.86 A; A=1-136.
DR PDB; 4RRK; X-ray; 1.86 A; A=1-136.
DR PDB; 4RRL; X-ray; 1.97 A; A=1-136.
DR PDB; 4RRM; X-ray; 1.55 A; A=1-136.
DR PDBsum; 4RR6; -.
DR PDBsum; 4RR7; -.
DR PDBsum; 4RR8; -.
DR PDBsum; 4RR9; -.
DR PDBsum; 4RRA; -.
DR PDBsum; 4RRB; -.
DR PDBsum; 4RRC; -.
DR PDBsum; 4RRD; -.
DR PDBsum; 4RRH; -.
DR PDBsum; 4RRI; -.
DR PDBsum; 4RRJ; -.
DR PDBsum; 4RRK; -.
DR PDBsum; 4RRL; -.
DR PDBsum; 4RRM; -.
DR AlphaFoldDB; Q9YFY3; -.
DR SMR; Q9YFY3; -.
DR STRING; 272557.APE_0117.1; -.
DR EnsemblBacteria; BAA79028; BAA79028; APE_0117.1.
DR KEGG; ape:APE_0117.1; -.
DR eggNOG; arCOG00401; Archaea.
DR Proteomes; UP000002518; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0004829; F:threonine-tRNA ligase activity; IEA:InterPro.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.800; -; 1.
DR Gene3D; 3.50.80.10; -; 1.
DR InterPro; IPR004154; Anticodon-bd.
DR InterPro; IPR036621; Anticodon-bd_dom_sf.
DR InterPro; IPR023509; DTD-like_sf.
DR InterPro; IPR015011; Threonyl-tRNA_syn_edit_dom_arc.
DR Pfam; PF03129; HGTP_anticodon; 1.
DR Pfam; PF08915; tRNA-Thr_ED; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Protein biosynthesis; Reference proteome;
KW RNA-binding; tRNA-binding.
FT CHAIN 1..421
FT /note="Threonine--tRNA ligase editing subunit"
FT /id="PRO_0000101118"
FT MUTAGEN 77
FT /note="H->A: Isolated domain has decreased deacylation of
FT mischarged L-seryl-tRNA(Thr), no activity on L-threonyl-
FT tRNA(Thr). Deacylates correctly charged glycyl-tRNA(Gly)."
FT /evidence="ECO:0000269|PubMed:26113036"
FT MUTAGEN 115
FT /note="Y->A: Whole protein and isolated domain have nearly
FT wild-type deacylation of mischarged L-seryl-tRNA(Thr), no
FT activity on L-threonyl-tRNA(Thr). Same results; when
FT associated with A-129."
FT /evidence="ECO:0000269|PubMed:26113036"
FT MUTAGEN 116
FT /note="K->M: Isolated domain does not deacylate mischarged
FT L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr)."
FT /evidence="ECO:0000269|PubMed:26113036"
FT MUTAGEN 129
FT /note="E->A: Whole protein and isolated domain have nearly
FT wild-type deacylation of mischarged L-seryl-tRNA(Thr), no
FT activity on L-threonyl-tRNA(Thr). Same results; when
FT associated with A-115."
FT /evidence="ECO:0000269|PubMed:26113036"
FT STRAND 2..22
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 29..41
FT /evidence="ECO:0007829|PDB:4RRI"
FT HELIX 48..65
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:4RRH"
FT HELIX 85..99
FT /evidence="ECO:0007829|PDB:4RRI"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 105..109
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 112..122
FT /evidence="ECO:0007829|PDB:4RRI"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:4RRI"
SQ SEQUENCE 421 AA; 45003 MW; 9B311637CE9FBC73 CRC64;
MRLLYLHADR FEYKTVKPAL KNPPDPPGEA SFGEALVVFT TVEDGDGPQT VMYAASDIAS
HSSRLKVTTV ILYPYAHLSS RLAKPMAAHK RLIELEGALR TKFPGHVHRA PFGWYKSFSI
ACKGHPLAEL SRSFTEAGAL QPWPAVEDYK TGLSGEVLAR AGLLGGGSLS PASWALEVHR
RLAEEVVGPA ESVGFGESLS EAYQACISSS VTTLLMGPYP PSIVFGPLED DPVEAVSRVL
GLISPQLEGV KPLLSGGEGA LKASSPDGAE LPVAFLKEGR VCLGPTLSFF KLAVSMLVEK
ARKEGLTPYL NPTLTPVQSA VIPVDSESEG YAQRIAEDLA ASGVRVSIVR GSGLGRRVRE
AGRSWASLVI VVGKREEETG TVVVRRRWEP GKQEVLTLDE LSSEAKKLAS GSRGSLYSTT
L
