PYLB_METBF
ID PYLB_METBF Reviewed; 350 AA.
AC Q46E78;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=Mbar_A0838;
OS Methanosarcina barkeri (strain Fusaro / DSM 804).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=269797;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Fusaro / DSM 804;
RX PubMed=16980466; DOI=10.1128/jb.00810-06;
RA Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S.,
RA Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.;
RT "The Methanosarcina barkeri genome: comparative analysis with
RT Methanosarcina acetivorans and Methanosarcina mazei reveals extensive
RT rearrangement within methanosarcinal genomes.";
RL J. Bacteriol. 188:7922-7931(2006).
RN [2]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH 4FE-4S CLUSTER;
RP S-ADENOSYL-L-METHIONINE AND REACTION PRODUCT, FUNCTION, COFACTOR, PATHWAY,
RP AND PUTATIVE REACTION MECHANISM.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=22095926; DOI=10.1002/anie.201106765;
RA Quitterer F., List A., Eisenreich W., Bacher A., Groll M.;
RT "Crystal structure of methylornithine synthase (PylB): insights into the
RT pyrrolysine biosynthesis.";
RL Angew. Chem. Int. Ed. 51:1339-1342(2012).
CC -!- FUNCTION: Catalyzes the isomerization of L-lysine to (2R,3R)-3-
CC methylornithine via a radical-based mechanism, a step in the
CC biosynthesis pathway of pyrrolysine. {ECO:0000269|PubMed:21455182,
CC ECO:0000269|PubMed:22095926}.
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 Evidence={ECO:0000269|PubMed:21455182};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:22095926};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:22095926};
CC -!- COFACTOR:
CC Name=S-adenosyl-L-methionine; Xref=ChEBI:CHEBI:59789;
CC Evidence={ECO:0000269|PubMed:22095926};
CC Note=Binds 1 S-adenosyl-L-methionine per subunit.
CC {ECO:0000269|PubMed:22095926};
CC -!- PATHWAY: Amino-acid biosynthesis; L-pyrrolysine biosynthesis.
CC {ECO:0000269|PubMed:22095926}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. PylB family.
CC {ECO:0000305}.
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DR EMBL; CP000099; AAZ69814.1; -; Genomic_DNA.
DR RefSeq; WP_011305864.1; NC_007355.1.
DR PDB; 3T7V; X-ray; 1.50 A; A=1-350.
DR PDBsum; 3T7V; -.
DR AlphaFoldDB; Q46E78; -.
DR SMR; Q46E78; -.
DR STRING; 269797.Mbar_A0838; -.
DR EnsemblBacteria; AAZ69814; AAZ69814; Mbar_A0838.
DR GeneID; 3625576; -.
DR KEGG; mba:Mbar_A0838; -.
DR eggNOG; arCOG00658; Archaea.
DR HOGENOM; CLU_033172_0_0_2; -.
DR OMA; IMGFNPY; -.
DR OrthoDB; 35292at2157; -.
DR BioCyc; MetaCyc:MON-17153; -.
DR BRENDA; 5.4.99.58; 3250.
DR UniPathway; UPA01028; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0016866; F:intramolecular transferase activity; IDA:UniProtKB.
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; IDA: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 3D-structure; 4Fe-4S; Amino-acid biosynthesis; Iron; Iron-sulfur;
KW Isomerase; Metal-binding; S-adenosyl-L-methionine.
FT CHAIN 1..350
FT /note="3-methylornithine synthase"
FT /id="PRO_0000420349"
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 BINDING 75
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 77
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22095926"
FT BINDING 78
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 112
FT /ligand="substrate"
FT BINDING 146
FT /ligand="substrate"
FT BINDING 169
FT /ligand="substrate"
FT BINDING 171
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22095926"
FT BINDING 182
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22095926"
FT BINDING 190
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22095926"
FT BINDING 235
FT /ligand="substrate"
FT BINDING 240
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22095926"
FT BINDING 277..279
FT /ligand="substrate"
FT BINDING 298..299
FT /ligand="substrate"
FT HELIX 13..18
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 25..32
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 37..55
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 58..68
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 93..103
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 109..115
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 119..123
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 126..139
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 152..160
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 175..181
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 203..213
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 216..228
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:3T7V"
FT TURN 246..249
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 258..268
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 275..277
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 278..291
FT /evidence="ECO:0007829|PDB:3T7V"
FT STRAND 296..300
FT /evidence="ECO:0007829|PDB:3T7V"
FT TURN 313..316
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 324..334
FT /evidence="ECO:0007829|PDB:3T7V"
FT HELIX 341..345
FT /evidence="ECO:0007829|PDB:3T7V"
SQ SEQUENCE 350 AA; 40009 MW; B9DA379864F087E3 CRC64;
MIQKMALDEF DSLGDKVIEG YQLTDNDLRT LLSLESKEGL ERLYSAARKV RDHYFGNRVF
LNCFIYFSTY CKNQCSFCYY NCRNEINRYR LTMEEIKETC KTLKGAGFHM VDLTMGEDPY
YYEDPNRFVE LVQIVKEELG LPIMISPGLM DNATLLKARE KGANFLALYQ ETYDTELYRK
LRVGQSFDGR VNARRFAKQQ GYCVEDGILT GVGNDIESTI LSLRGMSTND PDMVRVMTFL
PQEGTPLEGF RDKSNLSELK IISVLRLMFP KRLIPASLDL EGIDGMVLRL NAGANIVTSI
LPPDSQLEGV ANYDRDLEER DRDIKSVVRR LEIMGMKPAR QADFEAVLGC
