PYLB_METAC
ID PYLB_METAC Reviewed; 350 AA.
AC Q8TUB9;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=3-methylornithine synthase;
DE EC=5.4.99.58;
DE AltName: Full=(2R,3R)-3-methylornithine synthase;
DE AltName: Full=(3R)-3-methyl-D-ornithine synthase;
DE AltName: Full=Pyrrolysine biosynthesis protein PylB;
GN Name=pylB; OrderedLocusNames=MA_0154;
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: Catalyzes the isomerization of L-lysine to (2R,3R)-3-
CC methylornithine via a radical-based mechanism (Probable). Is required
CC for the biosynthesis of pyrrolysine. {ECO:0000269|PubMed:17204561,
CC ECO:0000269|PubMed:21455182, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysine = (3R)-3-methyl-D-ornithine; Xref=Rhea:RHEA:32759,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:64642; EC=5.4.99.58;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. {ECO:0000250};
CC -!- COFACTOR:
CC Name=S-adenosyl-L-methionine; Xref=ChEBI:CHEBI:59789;
CC Evidence={ECO:0000250};
CC Note=Binds 1 S-adenosyl-L-methionine per subunit. {ECO:0000250};
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 radical SAM superfamily. PylB family.
CC {ECO:0000305}.
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DR EMBL; AE010299; AAM03607.1; -; Genomic_DNA.
DR RefSeq; WP_011020212.1; NC_003552.1.
DR AlphaFoldDB; Q8TUB9; -.
DR SMR; Q8TUB9; -.
DR STRING; 188937.MA_0154; -.
DR EnsemblBacteria; AAM03607; AAM03607; MA_0154.
DR GeneID; 1472046; -.
DR KEGG; mac:MA_0154; -.
DR HOGENOM; CLU_033172_0_0_2; -.
DR InParanoid; Q8TUB9; -.
DR OMA; IMGFNPY; -.
DR OrthoDB; 35292at2157; -.
DR PhylomeDB; Q8TUB9; -.
DR UniPathway; UPA01028; -.
DR Proteomes; UP000002487; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; ISS:UniProtKB.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016740; F:transferase activity; IBA:GO_Central.
DR GO; GO:0016765; F:transferase activity, transferring alkyl or aryl (other than methyl) groups; IDA:UniProtKB.
DR GO; GO:0008652; P:cellular amino acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0071524; P:pyrrolysine biosynthetic process; IMP:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR034422; HydE/PylB-like.
DR InterPro; IPR023891; Pyrrolys_PylB.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR43726; PTHR43726; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR SFLD; SFLDF00349; 3-methylornithine_synthase_(Py; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR03910; pyrrolys_PylB; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Amino-acid biosynthesis; Iron; Iron-sulfur; Isomerase;
KW Metal-binding; Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..350
FT /note="3-methylornithine synthase"
FT /id="PRO_0000420350"
FT DOMAIN 57..279
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 71
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
FT BINDING 75
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
FT BINDING 77
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 78
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 146
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 169
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 182
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 190
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 240
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 277..279
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 298..299
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 350 AA; 40363 MW; CA15A12ABAAF2A76 CRC64;
MIKKMATEDL DRFGEKIIEG FQLSDDDLRA LLSLESEEEL EKLYYVARKV RNHYFGNRVF
LNCFIYFSTY CKNQCAFCYY NCKNEINRYR LSREEIKETC KALKGAGFHM IDLTMGEDPY
YYEEPDRFVE LVQMVKNELG LPIMISPGVM DNATLLKARE KGANFFALYQ ETYDQELYEK
LRVGQSFKGR YNTRRFAKEQ GYCIEDGILT GVGNDIESTI KSLRGMKSND PDMVRVMTFL
PQEGTPLERF KENSNLSELK IIAILRLIFP KCLIPASLDL EGIDGMVHRL NAGANIVTSI
LPSDSKLEGV ANYDRDLEER DRDIKSVIKR LEGMGMEPAP QAEFETVLRC
