PYLC_METAC
ID PYLC_METAC Reviewed; 363 AA.
AC Q8TUC0;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=3-methyl-D-ornithine--L-lysine ligase {ECO:0000305};
DE EC=6.3.2.59 {ECO:0000269|PubMed:21455182};
DE AltName: Full=(3R)-3-methyl-D-ornithine:L-lysine ligase;
DE AltName: Full=Pyrrolysine biosynthesis protein PylC;
GN Name=pylC {ECO:0000303|PubMed:17204561}; OrderedLocusNames=MA_0153;
OS Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 /
OS C2A).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=188937;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX PubMed=11932238; DOI=10.1101/gr.223902;
RA Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W.,
RA Calvo S., Engels R., Smirnov S., Atnoor D., Brown A., Allen N., Naylor J.,
RA Stange-Thomann N., DeArellano K., Johnson R., Linton L., McEwan P.,
RA McKernan K., Talamas J., Tirrell A., Ye W., Zimmer A., Barber R.D.,
RA Cann I., Graham D.E., Grahame D.A., Guss A.M., Hedderich R.,
RA Ingram-Smith C., Kuettner H.C., Krzycki J.A., Leigh J.A., Li W., Liu J.,
RA Mukhopadhyay B., Reeve J.N., Smith K., Springer T.A., Umayam L.A.,
RA White O., White R.H., de Macario E.C., Ferry J.G., Jarrell K.F., Jing H.,
RA Macario A.J.L., Paulsen I.T., Pritchett M., Sowers K.R., Swanson R.V.,
RA Zinder S.H., Lander E., Metcalf W.W., Birren B.;
RT "The genome of Methanosarcina acetivorans reveals extensive metabolic and
RT physiological diversity.";
RL Genome Res. 12:532-542(2002).
RN [2]
RP FUNCTION IN PYRROLYSINE BIOSYNTHESIS, GENE NAME, PATHWAY, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX PubMed=17204561; DOI=10.1073/pnas.0610294104;
RA Longstaff D.G., Larue R.C., Faust J.E., Mahapatra A., Zhang L.,
RA Green-Church K.B., Krzycki J.A.;
RT "A natural genetic code expansion cassette enables transmissible
RT biosynthesis and genetic encoding of pyrrolysine.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1021-1026(2007).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX PubMed=21455182; DOI=10.1038/nature09918;
RA Gaston M.A., Zhang L., Green-Church K.B., Krzycki J.A.;
RT "The complete biosynthesis of the genetically encoded amino acid
RT pyrrolysine from lysine.";
RL Nature 471:647-650(2011).
CC -!- FUNCTION: Is required for the biosynthesis of pyrrolysine
CC (PubMed:17204561, PubMed:21455182). Catalyzes the ATP-dependent
CC ligation between (3R)-3-methyl-D-ornithine and L-lysine, leading to
CC (3R)-3-methyl-D-ornithyl-N6-L-lysine (PubMed:21455182).
CC {ECO:0000269|PubMed:17204561, ECO:0000269|PubMed:21455182}.
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:21455182};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32764;
CC Evidence={ECO:0000269|PubMed:21455182};
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:0000269|PubMed:17204561, ECO:0000269|PubMed:21455182}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to translate
CC UAG as pyrrolysine, and do not produce pyrrolysine.
CC {ECO:0000269|PubMed:17204561}.
CC -!- SIMILARITY: Belongs to the PylC family. {ECO:0000305}.
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DR EMBL; AE010299; AAM03606.1; -; Genomic_DNA.
DR RefSeq; WP_011020211.1; NC_003552.1.
DR AlphaFoldDB; Q8TUC0; -.
DR SMR; Q8TUC0; -.
DR STRING; 188937.MA_0153; -.
DR EnsemblBacteria; AAM03606; AAM03606; MA_0153.
DR GeneID; 1472045; -.
DR KEGG; mac:MA_0153; -.
DR HOGENOM; CLU_707177_0_0_2; -.
DR OMA; IMDVEAI; -.
DR OrthoDB; 61259at2157; -.
DR BioCyc; MetaCyc:MON-17155; -.
DR BRENDA; 6.3.2.59; 7224.
DR UniPathway; UPA01028; -.
DR Proteomes; UP000002487; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IMP:UniProtKB.
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..363
FT /note="3-methyl-D-ornithine--L-lysine ligase"
FT /id="PRO_0000420351"
FT DOMAIN 85..269
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 10
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 11..12
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 31
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 49..50
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 72..73
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 72
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 104
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 131
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 138
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 160..163
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 169..171
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 225
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 227
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 239
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 243..248
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 246
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 302
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
FT BINDING 302
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000250|UniProtKB:Q46E79"
SQ SEQUENCE 363 AA; 40864 MW; D67AAF6A2D738D4D CRC64;
MKTICLIGGK LQGFEAAYLS KKADMKVVVI DKNPQALIRN YADEFHCFDV IKEPEKLLEI
SKNVDAILPV NENLECIKFL SSVKEEFSCP VLFDFEAYRI SRDKKKSKEY FRSIGIPTPQ
DKPGRPPYFV KPPCESSSVG ARIIYDEEEL GELEPGMLVE EYVEGEVISL EVIGDGTHFA
VVKETLIHID RTYDCHMVTP LPSDLSFREI SYSLAANLPL KGIMDVEAIS GPQGLKVIEI
DSRFPSQTPT AVYYSSGVNL IELLFRAFGE GVEEVKTLPE DRYCIYEHLM LAENGALIPV
GEQVLSMGND YGKYYEEPGI EIFLCRGEDP VFTLVFWGKD REEAENKKRT GLLILKDRFG
AAV
