PYLC_METBF
ID PYLC_METBF Reviewed; 363 AA.
AC Q46E79;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=3-methyl-D-ornithine--L-lysine ligase {ECO:0000305};
DE EC=6.3.2.59 {ECO:0000305|PubMed:22985965};
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:22985965};
GN OrderedLocusNames=Mbar_A0837 {ECO:0000312|EMBL:AAZ69813.1};
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] {ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM, ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO, ECO:0007744|PDB:4FFP, ECO:0007744|PDB:4FFR}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH ADP; ATP;
RP D-ORNITHINE; L-LYSINE; L-LYSINE-N(EPSILON)-D-ORNITHINE AND MAGNESIUM,
RP REACTION MECHANISM, COFACTOR, AND DOMAIN.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=22985965; DOI=10.1016/j.jmb.2012.09.007;
RA Quitterer F., List A., Beck P., Bacher A., Groll M.;
RT "Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine:
RT structure and reaction mechanism of PylC at 1.5A resolution.";
RL J. Mol. Biol. 424:270-282(2012).
CC -!- FUNCTION: Is required for the biosynthesis of pyrrolysine (By
CC similarity). 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 (Probable). {ECO:0000250|UniProtKB:Q8TUC0,
CC ECO:0000305|PubMed:22985965}.
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:0000305|PubMed:22985965};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32764;
CC Evidence={ECO:0000305|PubMed:22985965};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:22985965};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000269|PubMed:22985965};
CC -!- PATHWAY: Amino-acid biosynthesis; L-pyrrolysine biosynthesis.
CC {ECO:0000250|UniProtKB:Q8TUC0}.
CC -!- DOMAIN: Contains two adenine nucleotides bound at the active site. One
CC ATP molecule is involved in catalysis, the second adenine nucleotide
CC functions as a selective anchor for the C- and N-terminus of the Lys
CC substrate and is responsible for protein stability.
CC {ECO:0000269|PubMed:22985965}.
CC -!- SIMILARITY: Belongs to the PylC family. {ECO:0000305}.
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DR EMBL; CP000099; AAZ69813.1; -; Genomic_DNA.
DR PDB; 4FFL; X-ray; 1.50 A; A=1-363.
DR PDB; 4FFM; X-ray; 1.91 A; A=1-363.
DR PDB; 4FFN; X-ray; 2.40 A; A=1-363.
DR PDB; 4FFO; X-ray; 2.00 A; A=1-363.
DR PDB; 4FFP; X-ray; 2.00 A; A=1-363.
DR PDB; 4FFR; X-ray; 1.80 A; A=1-363.
DR PDBsum; 4FFL; -.
DR PDBsum; 4FFM; -.
DR PDBsum; 4FFN; -.
DR PDBsum; 4FFO; -.
DR PDBsum; 4FFP; -.
DR PDBsum; 4FFR; -.
DR SMR; Q46E79; -.
DR STRING; 269797.Mbar_A0837; -.
DR EnsemblBacteria; AAZ69813; AAZ69813; Mbar_A0837.
DR KEGG; mba:Mbar_A0837; -.
DR eggNOG; arCOG01596; Archaea.
DR HOGENOM; CLU_707177_0_0_2; -.
DR OMA; IMDVEAI; -.
DR BRENDA; 6.3.2.59; 3250.
DR UniPathway; UPA01028; -.
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 3D-structure; Amino-acid biosynthesis; ATP-binding; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding.
FT CHAIN 1..363
FT /note="3-methyl-D-ornithine--L-lysine ligase"
FT /id="PRO_0000454906"
FT BINDING 10
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFR"
FT BINDING 11..12
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL"
FT BINDING 31
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFR"
FT BINDING 49..50
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFR"
FT BINDING 72..73
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFR"
FT BINDING 72
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL"
FT BINDING 104
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFO, ECO:0007744|PDB:4FFP"
FT BINDING 131
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFO, ECO:0007744|PDB:4FFP"
FT BINDING 138
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFP"
FT BINDING 160..163
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFO, ECO:0007744|PDB:4FFP"
FT BINDING 169..171
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFN"
FT BINDING 225
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFN"
FT BINDING 227
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFP, ECO:0007744|PDB:4FFR"
FT BINDING 239
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFO, ECO:0007744|PDB:4FFP"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFP, ECO:0007744|PDB:4FFR"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFP, ECO:0007744|PDB:4FFR"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL, ECO:0007744|PDB:4FFM,
FT ECO:0007744|PDB:4FFN, ECO:0007744|PDB:4FFO,
FT ECO:0007744|PDB:4FFP, ECO:0007744|PDB:4FFR"
FT BINDING 243..248
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFN"
FT BINDING 246
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL"
FT BINDING 302
FT /ligand="D-ornithine"
FT /ligand_id="ChEBI:CHEBI:57668"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFN"
FT BINDING 302
FT /ligand="L-lysine"
FT /ligand_id="ChEBI:CHEBI:32551"
FT /evidence="ECO:0000269|PubMed:22985965,
FT ECO:0007744|PDB:4FFL"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 11..22
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 26..32
FT /evidence="ECO:0007829|PDB:4FFL"
FT TURN 37..41
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 42..47
FT /evidence="ECO:0007829|PDB:4FFL"
FT TURN 50..52
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 54..61
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 63..69
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 74..83
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 104..113
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 128..131
FT /evidence="ECO:0007829|PDB:4FFL"
FT TURN 137..140
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 165..177
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 185..189
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 195..200
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 205..216
FT /evidence="ECO:0007829|PDB:4FFL"
FT TURN 217..219
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 221..231
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 234..241
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 248..256
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 260..267
FT /evidence="ECO:0007829|PDB:4FFL"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 283..291
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 296..299
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 302..305
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 309..317
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 320..329
FT /evidence="ECO:0007829|PDB:4FFL"
FT STRAND 331..340
FT /evidence="ECO:0007829|PDB:4FFL"
FT HELIX 341..359
FT /evidence="ECO:0007829|PDB:4FFL"
SQ SEQUENCE 363 AA; 40816 MW; ED01018F5899D947 CRC64;
MKTICLVGGK LQGFEAAYLS KKAGMKVVLV DKNPQALIRN YADEFYCFDV IKEPEKLLEL
SKRVDAVLPV NENLACIEFL NSIKEKFSCP VLFDFEAYRI SRDKKKSKDY FKSIGVPTPQ
DRPSKPPYFV KPPCESSSVG ARIIYDDKDL EGLEPDTLVE EYVEGEVVSL EVVGDGSHFA
VVKETLVHID ETYDCHMVTP LPANPLFRQI SHDLAANLPL KGIMDVEAIF GPKGLRVIEI
DARFPSQTPT VVYYSSGINL IELLFRAFTD GVEEIRAIPE NKYCIYEHLM FGENGVLIPV
GEQVLSMGSD YGKFYEEPGI EIFLCKGEYP VFTMVFWGKD REETGAKRCK GLSVLKERFG
AVL
