PYLS_METMA
ID PYLS_METMA Reviewed; 454 AA.
AC Q8PWY1;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 25-MAY-2022, entry version 138.
DE RecName: Full=Pyrrolysine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_01573};
DE EC=6.1.1.26 {ECO:0000255|HAMAP-Rule:MF_01573};
DE AltName: Full=Pyrrolysine--tRNA(Pyl) ligase;
DE AltName: Full=Pyrrolysyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_01573};
DE Short=PylRS {ECO:0000255|HAMAP-Rule:MF_01573};
GN Name=pylS {ECO:0000255|HAMAP-Rule:MF_01573}; OrderedLocusNames=MM_1445;
OS Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM
OS 11833 / OCM 88) (Methanosarcina frisia).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=192952;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88;
RX PubMed=12125824;
RA Deppenmeier U., Johann A., Hartsch T., Merkl R., Schmitz R.A.,
RA Martinez-Arias R., Henne A., Wiezer A., Baeumer S., Jacobi C.,
RA Brueggemann H., Lienard T., Christmann A., Boemecke M., Steckel S.,
RA Bhattacharyya A., Lykidis A., Overbeek R., Klenk H.-P., Gunsalus R.P.,
RA Fritz H.-J., Gottschalk G.;
RT "The genome of Methanosarcina mazei: evidence for lateral gene transfer
RT between Bacteria and Archaea.";
RL J. Mol. Microbiol. Biotechnol. 4:453-461(2002).
CC -!- FUNCTION: Catalyzes the attachment of pyrrolysine to tRNA(Pyl).
CC Pyrrolysine is a lysine derivative encoded by the termination codon
CC UAG. {ECO:0000255|HAMAP-Rule:MF_01573}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-
CC pyrrolysyl-tRNA(Pyl); Xref=Rhea:RHEA:19277, Rhea:RHEA-COMP:9720,
CC Rhea:RHEA-COMP:9721, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58499, ChEBI:CHEBI:78442, ChEBI:CHEBI:78556,
CC ChEBI:CHEBI:456215; EC=6.1.1.26; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01573};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01573}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_01573}.
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DR EMBL; AE008384; AAM31141.1; -; Genomic_DNA.
DR RefSeq; WP_011033391.1; NC_003901.1.
DR PDB; 2E3C; X-ray; 2.65 A; A=185-454.
DR PDB; 2Q7E; X-ray; 1.80 A; A=185-454.
DR PDB; 2Q7G; X-ray; 1.90 A; A=185-454.
DR PDB; 2Q7H; X-ray; 2.10 A; A=185-454.
DR PDB; 2ZCE; X-ray; 1.80 A; A=185-454.
DR PDB; 2ZIM; X-ray; 2.10 A; A=185-454.
DR PDB; 2ZIN; X-ray; 1.79 A; A=185-454.
DR PDB; 2ZIO; X-ray; 2.06 A; A=185-454.
DR PDB; 3QTC; X-ray; 1.75 A; A=185-454.
DR PDB; 3VQV; X-ray; 1.90 A; A=185-454.
DR PDB; 3VQW; X-ray; 2.40 A; A=185-454.
DR PDB; 3VQX; X-ray; 2.30 A; A/B/C/D=185-454.
DR PDB; 4BW9; X-ray; 2.35 A; A=185-454.
DR PDB; 4BWA; X-ray; 2.45 A; A=185-454.
DR PDB; 4CH3; X-ray; 2.28 A; A=185-454.
DR PDB; 4CH4; X-ray; 2.16 A; A=185-454.
DR PDB; 4CH5; X-ray; 2.20 A; A=185-454.
DR PDB; 4CH6; X-ray; 2.05 A; A=185-454.
DR PDB; 4CS2; X-ray; 1.90 A; A=188-454.
DR PDB; 4CS3; X-ray; 1.50 A; A=188-454.
DR PDB; 4CS4; X-ray; 1.35 A; A=188-454.
DR PDB; 4Q6G; X-ray; 2.25 A; A=188-454.
DR PDB; 4TQD; X-ray; 2.14 A; A=185-454.
DR PDB; 4TQF; X-ray; 2.71 A; A=185-454.
DR PDB; 4ZIB; X-ray; 2.05 A; A=185-454.
DR PDB; 5K1P; X-ray; 1.50 A; A=188-454.
DR PDB; 5K1X; X-ray; 1.95 A; A=188-454.
DR PDB; 5UD5; X-ray; 2.35 A; A/B=1-101.
DR PDB; 5V6X; X-ray; 2.76 A; A/B=1-101.
DR PDB; 6AAC; X-ray; 1.48 A; A=185-454.
DR PDB; 6AAD; X-ray; 1.44 A; A=185-454.
DR PDB; 6AAN; X-ray; 1.51 A; A=185-454.
DR PDB; 6AAO; X-ray; 1.40 A; A=185-454.
DR PDB; 6AAP; X-ray; 1.50 A; A=185-454.
DR PDB; 6AAQ; X-ray; 1.55 A; A=185-454.
DR PDB; 6AAZ; X-ray; 1.84 A; A=185-454.
DR PDB; 6AB0; X-ray; 1.44 A; A=185-454.
DR PDB; 6AB1; X-ray; 1.38 A; A=185-454.
DR PDB; 6AB2; X-ray; 1.40 A; A=185-454.
DR PDB; 6AB8; X-ray; 1.75 A; A=185-454.
DR PDB; 6ABK; X-ray; 1.58 A; A=185-454.
DR PDB; 6ABL; X-ray; 1.47 A; A=185-454.
DR PDB; 6ABM; X-ray; 1.37 A; A=185-454.
DR PDB; 6LY3; X-ray; 1.90 A; A=185-454.
DR PDB; 6LY6; X-ray; 2.50 A; A=185-454.
DR PDB; 6LY7; X-ray; 2.09 A; A=185-454.
DR PDB; 6LYA; X-ray; 1.59 A; A=185-454.
DR PDB; 6LYB; X-ray; 1.90 A; A=185-454.
DR PDBsum; 2E3C; -.
DR PDBsum; 2Q7E; -.
DR PDBsum; 2Q7G; -.
DR PDBsum; 2Q7H; -.
DR PDBsum; 2ZCE; -.
DR PDBsum; 2ZIM; -.
DR PDBsum; 2ZIN; -.
DR PDBsum; 2ZIO; -.
DR PDBsum; 3QTC; -.
DR PDBsum; 3VQV; -.
DR PDBsum; 3VQW; -.
DR PDBsum; 3VQX; -.
DR PDBsum; 4BW9; -.
DR PDBsum; 4BWA; -.
DR PDBsum; 4CH3; -.
DR PDBsum; 4CH4; -.
DR PDBsum; 4CH5; -.
DR PDBsum; 4CH6; -.
DR PDBsum; 4CS2; -.
DR PDBsum; 4CS3; -.
DR PDBsum; 4CS4; -.
DR PDBsum; 4Q6G; -.
DR PDBsum; 4TQD; -.
DR PDBsum; 4TQF; -.
DR PDBsum; 4ZIB; -.
DR PDBsum; 5K1P; -.
DR PDBsum; 5K1X; -.
DR PDBsum; 5UD5; -.
DR PDBsum; 5V6X; -.
DR PDBsum; 6AAC; -.
DR PDBsum; 6AAD; -.
DR PDBsum; 6AAN; -.
DR PDBsum; 6AAO; -.
DR PDBsum; 6AAP; -.
DR PDBsum; 6AAQ; -.
DR PDBsum; 6AAZ; -.
DR PDBsum; 6AB0; -.
DR PDBsum; 6AB1; -.
DR PDBsum; 6AB2; -.
DR PDBsum; 6AB8; -.
DR PDBsum; 6ABK; -.
DR PDBsum; 6ABL; -.
DR PDBsum; 6ABM; -.
DR PDBsum; 6LY3; -.
DR PDBsum; 6LY6; -.
DR PDBsum; 6LY7; -.
DR PDBsum; 6LYA; -.
DR PDBsum; 6LYB; -.
DR AlphaFoldDB; Q8PWY1; -.
DR SMR; Q8PWY1; -.
DR STRING; 192952.MM_1445; -.
DR EnsemblBacteria; AAM31141; AAM31141; MM_1445.
DR GeneID; 44088939; -.
DR GeneID; 66137122; -.
DR KEGG; mma:MM_1445; -.
DR PATRIC; fig|192952.21.peg.1671; -.
DR eggNOG; arCOG00413; Archaea.
DR HOGENOM; CLU_648316_0_0_2; -.
DR OMA; RPMLAPN; -.
DR BRENDA; 6.1.1.26; 3270.
DR EvolutionaryTrace; Q8PWY1; -.
DR Proteomes; UP000000595; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0043767; F:pyrrolysyl-tRNA synthetase activity; IEA:UniProtKB-EC.
DR GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR GO; GO:0006418; P:tRNA aminoacylation for protein translation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_01573; Pyl_tRNA_synth; 1.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR002319; Phenylalanyl-tRNA_Synthase.
DR InterPro; IPR012739; Pyrrolysyl-tRNA_ligase.
DR InterPro; IPR023877; Pyrrolysyl-tRNA_ligase_C.
DR InterPro; IPR023878; Pyrrolysyl-tRNA_ligase_N.
DR Pfam; PF01409; tRNA-synt_2d; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR02367; PylS_Cterm; 1.
DR TIGRFAMs; TIGR03912; PylS_Nterm; 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; Reference proteome.
FT CHAIN 1..454
FT /note="Pyrrolysine--tRNA ligase"
FT /id="PRO_0000260453"
FT REGION 102..138
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 123..138
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 6..13
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 21..32
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 35..40
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:5UD5"
FT HELIX 55..61
FT /evidence="ECO:0007829|PDB:5UD5"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:5UD5"
FT TURN 70..73
FT /evidence="ECO:0007829|PDB:5UD5"
FT HELIX 76..83
FT /evidence="ECO:0007829|PDB:5UD5"
FT HELIX 192..201
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:4CH3"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:6LYA"
FT HELIX 216..236
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 242..256
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 266..269
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 270..275
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 280..282
FT /evidence="ECO:0007829|PDB:6ABL"
FT HELIX 283..287
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:5K1X"
FT TURN 292..294
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:4TQD"
FT HELIX 302..312
FT /evidence="ECO:0007829|PDB:4CS4"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 318..329
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 335..337
FT /evidence="ECO:0007829|PDB:6AB2"
FT STRAND 340..351
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 356..370
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:4CS4"
FT TURN 382..384
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 385..392
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 395..403
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 406..411
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 417..423
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 424..432
FT /evidence="ECO:0007829|PDB:4CS4"
FT HELIX 437..440
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 444..447
FT /evidence="ECO:0007829|PDB:4CS4"
FT STRAND 450..452
FT /evidence="ECO:0007829|PDB:4CS4"
SQ SEQUENCE 454 AA; 50921 MW; D6BE5A812B5CA96E CRC64;
MDKKPLNTLI SATGLWMSRT GTIHKIKHHE VSRSKIYIEM ACGDHLVVNN SRSSRTARAL
RHHKYRKTCK RCRVSDEDLN KFLTKANEDQ TSVKVKVVSA PTRTKKAMPK SVARAPKPLE
NTEAAQAQPS GSKFSPAIPV STQESVSVPA SVSTSISSIS TGATASALVK GNTNPITSMS
APVQASAPAL TKSQTDRLEV LLNPKDEISL NSGKPFRELE SELLSRRKKD LQQIYAEERE
NYLGKLEREI TRFFVDRGFL EIKSPILIPL EYIERMGIDN DTELSKQIFR VDKNFCLRPM
LAPNLYNYLR KLDRALPDPI KIFEIGPCYR KESDGKEHLE EFTMLNFCQM GSGCTRENLE
SIITDFLNHL GIDFKIVGDS CMVYGDTLDV MHGDLELSSA VVGPIPLDRE WGIDKPWIGA
GFGLERLLKV KHDFKNIKRA ARSESYYNGI STNL
