SYS_PYRHO
ID SYS_PYRHO Reviewed; 455 AA.
AC O58441;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Serine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00176};
DE EC=6.1.1.11 {ECO:0000255|HAMAP-Rule:MF_00176};
DE AltName: Full=Seryl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00176};
DE Short=SerRS {ECO:0000255|HAMAP-Rule:MF_00176};
DE AltName: Full=Seryl-tRNA(Ser/Sec) synthetase {ECO:0000255|HAMAP-Rule:MF_00176};
GN Name=serS {ECO:0000255|HAMAP-Rule:MF_00176}; OrderedLocusNames=PH0710;
GN ORFNames=PHCF014;
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]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of PH0710.";
RL Submitted (JUN-2007) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser). Is also able
CC to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-
CC seryl-tRNA(Sec), which will be further converted into selenocysteinyl-
CC tRNA(Sec). {ECO:0000255|HAMAP-Rule:MF_00176}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-
CC seryl-tRNA(Ser); Xref=Rhea:RHEA:12292, Rhea:RHEA-COMP:9669,
CC Rhea:RHEA-COMP:9703, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00176};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-
CC seryl-tRNA(Sec); Xref=Rhea:RHEA:42580, Rhea:RHEA-COMP:9742,
CC Rhea:RHEA-COMP:10128, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00176};
CC -!- PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec)
CC biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_00176}.
CC -!- SUBUNIT: Homodimer. The tRNA molecule binds across the dimer.
CC {ECO:0000255|HAMAP-Rule:MF_00176}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00176}.
CC -!- DOMAIN: Consists of two distinct domains, a catalytic core and a N-
CC terminal extension that is involved in tRNA binding.
CC {ECO:0000255|HAMAP-Rule:MF_00176}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type-1 seryl-tRNA synthetase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_00176}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA29801.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000001; BAA29801.1; ALT_INIT; Genomic_DNA.
DR PIR; G71117; G71117.
DR RefSeq; WP_048053201.1; NC_000961.1.
DR PDB; 2DQ0; X-ray; 2.60 A; A/B=1-455.
DR PDB; 2ZR2; X-ray; 2.80 A; A/B=1-455.
DR PDB; 2ZR3; X-ray; 3.00 A; A/B=1-455.
DR PDBsum; 2DQ0; -.
DR PDBsum; 2ZR2; -.
DR PDBsum; 2ZR3; -.
DR AlphaFoldDB; O58441; -.
DR SMR; O58441; -.
DR STRING; 70601.3257118; -.
DR EnsemblBacteria; BAA29801; BAA29801; BAA29801.
DR GeneID; 1443040; -.
DR KEGG; pho:PH0710; -.
DR eggNOG; arCOG00403; Archaea.
DR OMA; SPCFRRE; -.
DR OrthoDB; 16385at2157; -.
DR BRENDA; 6.1.1.11; 5244.
DR UniPathway; UPA00906; UER00895.
DR EvolutionaryTrace; O58441; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004828; F:serine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006434; P:seryl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00770; SerRS_core; 1.
DR Gene3D; 1.10.287.40; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00176; Ser_tRNA_synth_type1; 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; IPR002317; Ser-tRNA-ligase_type_1.
DR InterPro; IPR015866; Ser-tRNA-synth_1_N.
DR InterPro; IPR042103; SerRS_1_N_sf.
DR InterPro; IPR033729; SerRS_core.
DR InterPro; IPR010978; tRNA-bd_arm.
DR PANTHER; PTHR11778; PTHR11778; 1.
DR Pfam; PF02403; Seryl_tRNA_N; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR PIRSF; PIRSF001529; Ser-tRNA-synth_IIa; 1.
DR PRINTS; PR00981; TRNASYNTHSER.
DR SUPFAM; SSF46589; SSF46589; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00414; serS; 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 Nucleotide-binding; Protein biosynthesis.
FT CHAIN 1..455
FT /note="Serine--tRNA ligase"
FT /id="PRO_0000122182"
FT BINDING 252..254
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT BINDING 283..285
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT BINDING 299
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT BINDING 306
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT BINDING 370..373
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT BINDING 406
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00176"
FT HELIX 4..9
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 24..28
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 29..65
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 72..103
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 139..146
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 175..180
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 190..209
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 223..227
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 234..237
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 240..242
FT /evidence="ECO:0007829|PDB:2ZR3"
FT HELIX 254..259
FT /evidence="ECO:0007829|PDB:2DQ0"
FT TURN 260..263
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 264..267
FT /evidence="ECO:0007829|PDB:2DQ0"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 272..282
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 289..292
FT /evidence="ECO:0007829|PDB:2ZR3"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 300..311
FT /evidence="ECO:0007829|PDB:2DQ0"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 316..333
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 338..342
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 345..347
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 353..362
FT /evidence="ECO:0007829|PDB:2DQ0"
FT TURN 363..366
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 367..376
FT /evidence="ECO:0007829|PDB:2DQ0"
FT TURN 378..381
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 382..385
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 387..392
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 401..409
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 410..420
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 432..434
FT /evidence="ECO:0007829|PDB:2DQ0"
FT HELIX 435..438
FT /evidence="ECO:0007829|PDB:2DQ0"
FT STRAND 441..443
FT /evidence="ECO:0007829|PDB:2DQ0"
SQ SEQUENCE 455 AA; 53255 MW; B8D8A418A0651710 CRC64;
MLDIKLIREN PELVKNDLIK RGELEKVKWV DEILKLDTEW RTKLKEINRL RHERNKIAVE
IGKRRKKGEP VDELLAKSRE IVKRIGELEN EVEELKKKID YYLWRLPNIT HPSVPVGKDE
NDNVPIRFWG KARVWKGHLE RFLEQSQGKM EYEILEWKPK LHVDLLEILG GADFARAAKV
SGSRFYYLLN EIVILDLALI RFALDRLIEK GFTPVIPPYM VRRFVEEGST SFEDFEDVIY
KVEDEDLYLI PTAEHPLAGM HANEILDGKD LPLLYVGVSP CFRKEAGTAG KDTKGIFRVH
QFHKVEQFVY SRPEESWEWH EKIIRNAEEL FQELEIPYRV VNICTGDLGY VAAKKYDIEA
WMPGQGKFRE VVSASNCTDW QARRLNIRFR DRTDEKPRYV HTLNSTAIAT SRAIVAILEN
HQEEDGTVRI PKVLWKYTGF KEIVPVEKKE RCCAT
