PYLC_METMA
ID PYLC_METMA Reviewed; 371 AA.
AC Q8PWY3;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=3-methyl-D-ornithine--L-lysine ligase {ECO:0000305};
DE EC=6.3.2.59 {ECO:0000269|PubMed:21525873};
DE AltName: Full=(3R)-3-methyl-D-ornithine:L-lysine ligase {ECO:0000305};
DE AltName: Full=Pyrrolysine biosynthesis protein PylC {ECO:0000305};
GN Name=pylC {ECO:0000303|PubMed:21525873};
GN OrderedLocusNames=MM_1443 {ECO:0000312|EMBL:AAM31139.1};
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).
RN [2]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=21525873; DOI=10.1038/nchembio.586;
RA Cellitti S.E., Ou W., Chiu H.P., Gruenewald J., Jones D.H., Hao X., Fan Q.,
RA Quinn L.L., Ng K., Anfora A.T., Lesley S.A., Uno T., Brock A.,
RA Geierstanger B.H.;
RT "D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-
RT carboxy-lysine.";
RL Nat. Chem. Biol. 7:528-530(2011).
CC -!- FUNCTION: Is required for the biosynthesis of pyrrolysine
CC (PubMed:21525873). Catalyzes the ATP-dependent ligation between (3R)-3-
CC methyl-D-ornithine and L-lysine, leading to (3R)-3-methyl-D-ornithyl-
CC N6-L-lysine (PubMed:21525873). Is also involved in the synthesis of
CC pyrroline-carboxy-lysine (Pcl), a demethylated form of pyrrolysine that
CC is generated by the pyrrolysine biosynthetic enzymes when the growth
CC media is supplemented with D-ornithine (PubMed:21525873).
CC {ECO:0000269|PubMed:21525873}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3R)-3-methyl-D-ornithine + ATP + L-lysine = (3R)-3-methyl-D-
CC ornithyl-N(6)-L-lysine + ADP + H(+) + phosphate;
CC Xref=Rhea:RHEA:32763, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:43474, ChEBI:CHEBI:64642,
CC ChEBI:CHEBI:64643, ChEBI:CHEBI:456216; EC=6.3.2.59;
CC Evidence={ECO:0000269|PubMed:21525873};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32764;
CC Evidence={ECO:0000269|PubMed:21525873};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q46E79};
CC Note=Binds 2 magnesium ions per subunit.
CC {ECO:0000250|UniProtKB:Q46E79};
CC -!- PATHWAY: Amino-acid biosynthesis; L-pyrrolysine biosynthesis.
CC {ECO:0000305|PubMed:21525873}.
CC -!- SIMILARITY: Belongs to the PylC family. {ECO:0000305}.
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DR EMBL; AE008384; AAM31139.1; -; Genomic_DNA.
DR RefSeq; WP_011033389.1; NC_003901.1.
DR SMR; Q8PWY3; -.
DR STRING; 192952.MM_1443; -.
DR EnsemblBacteria; AAM31139; AAM31139; MM_1443.
DR GeneID; 24879563; -.
DR KEGG; mma:MM_1443; -.
DR PATRIC; fig|192952.21.peg.1669; -.
DR eggNOG; arCOG01596; Archaea.
DR HOGENOM; CLU_707177_0_0_2; -.
DR OMA; IMDVEAI; -.
DR UniPathway; UPA01028; -.
DR Proteomes; UP000000595; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008652; P:cellular amino acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0071524; P:pyrrolysine biosynthetic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR003806; ATP-grasp_PylC-type.
DR InterPro; IPR023890; Pyrrolys_PylC.
DR Pfam; PF02655; ATP-grasp_3; 1.
DR TIGRFAMs; TIGR03909; pyrrolys_PylC; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; ATP-binding; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..371
FT /note="3-methyl-D-ornithine--L-lysine ligase"
FT /id="PRO_0000454907"
FT DOMAIN 93..277
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 19..20
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 39
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 57..58
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 80..81
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 80
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 112
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 139
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 146
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 168..171
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 177..179
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 233
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 247
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 251..256
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 254
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 310
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 310
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
SQ SEQUENCE 371 AA; 41516 MW; C33300755F614F9F CRC64;
MRESWGASLK TICLIGGKLQ GFEAAYLSKK AGMKVLVIDK NPQALIRNYA DEFQCFNITE
EPEKLVAISK NVDAILPVNE NLECIEFLNS IKEKFSCPVL FDFEAYRISR DKRKSKEYFA
SIGTPTPQDK PSEPPYFVKP PCESSSVGAR IIHDRKELKE LEPGMLIEEY VEGEVVSLEV
IGDGNNFAVV KETLVHIDDT YDCHMVTPLP LDPSFRELSY SLAANLPLKG IMDVEAISGP
LGLKVIEIDA RFPSQTPTAV YYSSGINLIE LLFRAFNGGI EEIKTLPEDR YCIYEHLMLA
ENGVLIPVGE QVLSMGNDYG NYYEEPGIEI FLCKGENPVF TLVFWGRDRE EAEARKNKGL
SILKSRFGAA A
