ID   PYLD_METAC              Reviewed;         259 AA.
AC   Q8TUC1;
DT   28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   25-MAY-2022, entry version 79.
DE   RecName: Full=3-methylornithyl-N6-L-lysine dehydrogenase;
DE            EC=1.4.1.-;
DE   AltName: Full=(3R)-3-methyl-D-ornithyl-N6-L-lysine dehydrogenase;
DE   AltName: Full=Pyrrolysine biosynthesis protein PylD;
GN   Name=pylD; OrderedLocusNames=MA_0152;
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, AND DISRUPTION 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, 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: Likely catalyzes the NAD(P)-dependent oxidative deamination
CC       of (3R)-3-methyl-D-ornithyl-N6-L-lysine, resulting in the formation of
CC       pyrrolysine after spontaneous dehydration and cyclization of the
CC       intermediate. Is required for the biosynthesis of pyrrolysine.
CC       {ECO:0000269|PubMed:17204561, ECO:0000269|PubMed:21455182}.
CC   -!- PATHWAY: Amino-acid biosynthesis; L-pyrrolysine biosynthesis.
CC       {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 PylD family. {ECO:0000305}.
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DR   EMBL; AE010299; AAM03605.1; -; Genomic_DNA.
DR   RefSeq; WP_011020210.1; NC_003552.1.
DR   AlphaFoldDB; Q8TUC1; -.
DR   SMR; Q8TUC1; -.
DR   STRING; 188937.MA_0152; -.
DR   EnsemblBacteria; AAM03605; AAM03605; MA_0152.
DR   GeneID; 1472044; -.
DR   KEGG; mac:MA_0152; -.
DR   HOGENOM; CLU_089249_0_0_2; -.
DR   OMA; IILMADD; -.
DR   OrthoDB; 50677at2157; -.
DR   UniPathway; UPA01028; -.
DR   Proteomes; UP000002487; Chromosome.
DR   GO; GO:0016491; F:oxidoreductase activity; 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; IPR023914; Pyrrolys_PylD.
DR   TIGRFAMs; TIGR03911; pyrrolys_PylD; 1.
PE   1: Evidence at protein level;
KW   Amino-acid biosynthesis; NAD; NADP; Oxidoreductase; Reference proteome.
FT   CHAIN           1..259
FT                   /note="3-methylornithyl-N6-L-lysine dehydrogenase"
FT                   /id="PRO_0000420352"
SQ   SEQUENCE   259 AA;  28048 MW;  6E178700A17B3FFE CRC64;
     MALLTPEDLE NINRQLHEAD STVRRVTGLD IKGVCKDFYG TTPCCEKVGI VPVTSGNGII
     GNFSESLRAI TEYFGFDSFV TTMPDVSGYY EAVRNGAQII LMADDNTFLA HNLKNGKIAN
     NQPCTGIIYA EIASRYMKAD SKDVLAVGLG KVGFPGAAHL VNKGFRVYGY DADKALLEKT
     VSDLGITPFE PENPRRFSII FEATPCADTV PESVISDNCV ISTPGIPCAI SRELQEKYGV
     ELIMEPLGIG TASMLYSIL