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Information on EC 6.3.2.59 - 3-methyl-D-ornithine---L-lysine ligase
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6.3.2.59 3-methyl-D-ornithine---L-lysine ligaseIUBMB Comments
The enzyme participates in the biosynthesis of L-pyrrolysine, a naturally occurring, genetically coded amino acid found in some methanogenic archaea and a few bacterial species. L-pyrrolysine is present in several methyltransferases that are involved in methyl transfer from methylated amine compounds to coenzyme M.
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The expected taxonomic range for this enzyme is: Methanosarcinaceae
Reaction Schemes
Synonyms
atp-grasp domain-containing protein, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-methylornithine---L-lysine ligase
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3-methylornithine-L-lysine ligase
ATP-grasp domain-containing protein
Mbar_A0837
N6-[(2R,3R)-3-methylornithyl]-L-lysine synthase
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pylC
pylC
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP, structure-function relationship analysis. The binding of Lys to the enzyme complex is then followed by an SN2 reaction resulting in L-lysine-Nepsilon-D-ornithine and inorganic phosphate. PylC harbors two adenine nucleotides bound at the active site. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability
ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP, structure-function relationship analysis. The binding of Lys to the enzyme complex is then followed by an SN2 reaction resulting in L-lysine-Nepsilon-D-ornithine and inorganic phosphate. PylC harbors two adenine nucleotides bound at the active site. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability
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ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP, structure-function relationship analysis. The binding of Lys to the enzyme complex is then followed by an SN2 reaction resulting in L-lysine-Nepsilon-D-ornithine and inorganic phosphate. PylC harbors two adenine nucleotides bound at the active site. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability
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SYSTEMATIC NAME
IUBMB Comments
(3R)-3-methyl-D-ornithine:L-lysine gamma-ligase (ADP-forming)
The enzyme participates in the biosynthesis of L-pyrrolysine, a naturally occurring, genetically coded amino acid found in some methanogenic archaea and a few bacterial species. L-pyrrolysine is present in several methyltransferases that are involved in methyl transfer from methylated amine compounds to coenzyme M.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
additional information
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the amino acid, S-2-amino-6-(R-3,4-dihydro-2H-pyrrole-2-carboxamido)-hexanoic acid, named pyrroline-carboxy-lysine (Pcl), is only produced in high amounts in the presence of D-ornithine but, like Pyl, is a substrate for PylS for site-specific incorporation into proteins
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
Methanosarcina spp.
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
additional information
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the amino acid, S-2-amino-6-(R-3,4-dihydro-2H-pyrrole-2-carboxamido)-hexanoic acid, named pyrroline-carboxy-lysine (Pcl), is only produced in high amounts in the presence of D-ornithine but, like Pyl, is a substrate for PylS for site-specific incorporation into proteins
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
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ATP + (3R)-3-methyl-D-ornithine + L-lysine
ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
Methanosarcina spp.
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
evolution
PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
evolution
PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
evolution
Methanosarcina spp.
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
evolution
PylC is a member of the carbamoyl phosphate synthetase family of proteins forming amides between carbon dioxide (or carboxyl groups), and ammonia (or amines)
evolution
the overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes, but there exist unique structural and functional features for a topological control of successive substrate entry and product release. PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date
evolution
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PylC is a member of the carbamoyl phosphate synthetase family of proteins forming amides between carbon dioxide (or carboxyl groups), and ammonia (or amines)
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evolution
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the overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes, but there exist unique structural and functional features for a topological control of successive substrate entry and product release. PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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evolution
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PylC is a member of the carbamoyl phosphate synthetase family of proteins forming amides between carbon dioxide (or carboxyl groups), and ammonia (or amines)
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evolution
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PylC is a member of the carbamoyl phosphate synthetase family of proteins forming amides between carbon dioxide (or carboxyl groups), and ammonia (or amines)
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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evolution
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the overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes, but there exist unique structural and functional features for a topological control of successive substrate entry and product release. PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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evolution
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PylC has similarity to members of the carbamoyl phosphate synthetase family, including D-Ala, D-Ala ligase, and amide formation is in keeping with this phylogeny
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metabolism
in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
metabolism
in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
metabolism
in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
metabolism
Methanosarcina spp.
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
metabolism
proposed pathway for the biosynthesis of amino acids Pyl and S-2-amino-6-(R-3,4-dihydro-2H-pyrrole-2-carboxamido)-hexanoic acid, named pyrroline-carboxy-lysine (Pcl), overview. PylB does not act on Pcl or L-Lys-D-Orn but rather acts upstream of PylC and PylD. For this to occur, PylC and PylD must tolerate methylated intermediates. D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine
metabolism
proposed pathway of pyrrolysine biosynthesis by the products of pylB, pylC, and pylD from two molecules of lysine. Lysine is first used to make (2R, 3R) 3-methylornithine. After ligation to a second molecule of lysine, the terminal amine of the methylornithyl-Nepsilon-lysine intermediate is oxidized to an aldehyde. Spontaneous elimination of water forms pyrrolysine
metabolism
the second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by enzyme PylC that forms the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine
metabolism
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proposed pathway of pyrrolysine biosynthesis by the products of pylB, pylC, and pylD from two molecules of lysine. Lysine is first used to make (2R, 3R) 3-methylornithine. After ligation to a second molecule of lysine, the terminal amine of the methylornithyl-Nepsilon-lysine intermediate is oxidized to an aldehyde. Spontaneous elimination of water forms pyrrolysine
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metabolism
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the second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by enzyme PylC that forms the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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metabolism
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proposed pathway of pyrrolysine biosynthesis by the products of pylB, pylC, and pylD from two molecules of lysine. Lysine is first used to make (2R, 3R) 3-methylornithine. After ligation to a second molecule of lysine, the terminal amine of the methylornithyl-Nepsilon-lysine intermediate is oxidized to an aldehyde. Spontaneous elimination of water forms pyrrolysine
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metabolism
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proposed pathway of pyrrolysine biosynthesis by the products of pylB, pylC, and pylD from two molecules of lysine. Lysine is first used to make (2R, 3R) 3-methylornithine. After ligation to a second molecule of lysine, the terminal amine of the methylornithyl-Nepsilon-lysine intermediate is oxidized to an aldehyde. Spontaneous elimination of water forms pyrrolysine
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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metabolism
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the second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by enzyme PylC that forms the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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metabolism
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in the Methanosarcinaceae, and related species such as Methanococcoides burtonii, Methanohalophilus mahii, and Methanohalobium evestigatum, pyrrolysine is synthesized and incorporated into the methylamine methyltransferases, involved in metabolism of trimethylamine, dimethylamine, or monomethylamine, through the combined actions of the products of the pyl genes. The pylT gene encodes tRNAPyl whose CUA anticodon allows for amber codon translation. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly with pyrrolysine. The synthesis of pyrrolysine is carried out by the pylBCD gene products. Metabolism overview
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physiological function
enzyme Pylc catalyzes the biosynthesis of pyrrolysine C by formation of the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine. Pyrrolysine (Pyl) is the 22nd genetically encoded amino acid, and has been discovered as a building block of three proteins (MtmB, MtbB, and MttB) that are all involved in the catabolism of methylamines in the Methanosarcina family of methanogenic archaea and in some eubacteria
physiological function
PylC ligates the epsilonN of lysine to the carboxyl of D-ornithine as a first step in forming desmethylpyrrolysine
physiological function
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
physiological function
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
physiological function
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
physiological function
Methanosarcina spp.
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synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
physiological function
-
PylC ligates the epsilonN of lysine to the carboxyl of D-ornithine as a first step in forming desmethylpyrrolysine
-
physiological function
-
enzyme Pylc catalyzes the biosynthesis of pyrrolysine C by formation of the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine. Pyrrolysine (Pyl) is the 22nd genetically encoded amino acid, and has been discovered as a building block of three proteins (MtmB, MtbB, and MttB) that are all involved in the catabolism of methylamines in the Methanosarcina family of methanogenic archaea and in some eubacteria
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
physiological function
-
PylC ligates the epsilonN of lysine to the carboxyl of D-ornithine as a first step in forming desmethylpyrrolysine
-
physiological function
-
PylC ligates the epsilonN of lysine to the carboxyl of D-ornithine as a first step in forming desmethylpyrrolysine
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
physiological function
-
enzyme Pylc catalyzes the biosynthesis of pyrrolysine C by formation of the pseudopeptide L-lysine-Nepsilon-3R-methyl-D-ornithine. Pyrrolysine (Pyl) is the 22nd genetically encoded amino acid, and has been discovered as a building block of three proteins (MtmB, MtbB, and MttB) that are all involved in the catabolism of methylamines in the Methanosarcina family of methanogenic archaea and in some eubacteria
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
physiological function
-
synthesis of pyrrolysine is carried out by the pylBCD gene products. Formation of desmethylpyrrolysine (dmPyl) requires only PylC and PylD. PylC carries out ligation of D-ornithine to the terminal amine of lysine, as cells transformed with pylC produce D-ornithyl-epsilonN-lysine dependent on exogenous D-ornithine
-
additional information
analysis of the incorporation of Pcl and Pyl at TAG codons, tandem mass spectrometry
additional information
the enzyme structure analysis of the active site containing LysNepsilon-D-Orn, two ADP molecules, and phosphate, functional role of the nucleotide bound at the D1 domain, mutational analysis, overview. The active site of PylC appears as a crescent shaped cavity with a length of about 35 A
additional information
-
the enzyme structure analysis of the active site containing LysNepsilon-D-Orn, two ADP molecules, and phosphate, functional role of the nucleotide bound at the D1 domain, mutational analysis, overview. The active site of PylC appears as a crescent shaped cavity with a length of about 35 A
-
additional information
-
the enzyme structure analysis of the active site containing LysNepsilon-D-Orn, two ADP molecules, and phosphate, functional role of the nucleotide bound at the D1 domain, mutational analysis, overview. The active site of PylC appears as a crescent shaped cavity with a length of about 35 A
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PYLC_METAC
Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
363
0
40864
Swiss-Prot
-
PYLC_METBF
Methanosarcina barkeri (strain Fusaro / DSM 804)
363
0
40816
Swiss-Prot
-
PYLC_METMA
Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
371
0
41516
Swiss-Prot
-
D5E9G2_METMS
Methanohalophilus mahii (strain ATCC 35705 / DSM 5219 / SLP)
360
0
40883
TrEMBL
-
D7E781_METEZ
Methanohalobium evestigatum (strain ATCC BAA-1072 / DSM 3721 / NBRC 107634 / OCM 161 / Z-7303)
370
0
41897
TrEMBL
-
Q12UB8_METBU
Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)
362
0
41068
TrEMBL
-
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant detagged enzyme in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5'-adenylyl-beta-gamma-imidodiphosphate, ADP, D-ornithine (D-Orn), L-lysine (Lys), phosphorylated D-Orn, L-lysine-Nepsilon-D-ornithine, inorganic phosphate, carbonate, and Mg2+, sitting drop vapor diffusion method, mixing of equal volumes of 18 mg/ml protein solution containing 10 mM ATP for states I, II, and III-V, or 10 mM AMP-PNP for state II, and additionally 50 mM Lys and/or 50 mM D-Orn or 5 mM LysNepsilon-D-Orn, with reservoir solution containing 100 mM 4-morpholineethanesulfonic acid, pH 6.5, 200 mM MgCl2, and 25% PEG 4000, 20°C, 5 days, X-ray diffraction structure determination and analysis at 1.5-2.0 A resolution, multiwavelength anomalous dispersion (MAD) methods using a selenomethionine (SeMet) derivative, modeling
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
additional information
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
-
additional information
the Pyl operon in Methanosarcina species contains five genes encoding three biosynthetic enzymes (PylB, PylC and PylD), a specific pyrrolysyl-tRNA synthetase (PylS) and the tRNA (PylT). Transfer of these genes is necessary and sufficient to support incorporation of Pyl intoproteins in Escherichia coli at low yields. Addition of D-ornithine to culture medium has been shown to increase yields of full-length protein expression in Escherichia coli containing the Pyl synthesis genes. Development of plasmid systems with inducible promoters for high-level protein expression in both Escherichia coli and mammalian cells (HEK-293 cells) using genes from Methanosarcina mazei, overview. A new amino acid, S-2-amino-6-(R-3,4-dihydro-2H-pyrrole-2-carboxamido)-hexanoic acid, named pyrroline-carboxy-lysine (Pcl), is only produced in high amounts in the presence of D-ornithine but, like Pyl, is a substrate for PylS for site-specific incorporation into proteins
additional information
Methanosarcina spp.
-
Escherichia coli expressing archaeal pylTSBCD can incorporate biosynthesized pyrrolysine into protein, with pylBCD required to make the PylS substrate
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21 Tuner (DE3) by nickel affinity chromatography
recombinant His6-tagged PylC from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, removal of the His-tag by His6-SUMO protease, dialysis, and again nickel affinity chromatography, followed by ultrafiltration of the flow through
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene pylC or Mbar_A0837, encoded in the pylBCD operon, recombinant overexpression of His6-tagged PylC in Escherichia coli strain BL21(DE3)
gene pylC, recombinant expression of His-tagged enzyme from operon pylTSBCD in Escherichia coli strain BL21 Tuner (DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gaston, M.; Jiang, R.; Krzycki, J.
Functional context, biosynthesis, and genetic encoding of pyrrolysine
Curr. Opin. Microbiol.
14
342-349
2011
Methanosarcina spp., no activity in Desulfobacterium autotrophicum, Methanohalophilus mahii (D5E9G2), Methanohalobium evestigatum (D7E781), Methanococcoides burtonii (Q12UB8), Methanococcoides burtonii OCM 468 (Q12UB8), Methanococcoides burtonii ACE-M (Q12UB8), Methanococcoides burtonii NBRC 107633 (Q12UB8), Methanohalobium evestigatum DSM 3721 (D7E781), Methanohalophilus mahii ATCC 35705 (D5E9G2), Methanococcoides burtonii DSM 6242 (Q12UB8)
brenda
Quitterer, F.; List, A.; Beck, P.; Bacher, A.; Groll, M.
Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine structure and reaction mechanism of PylC at 1.5 A resolution
J. Mol. Biol.
424
270-282
2012
Methanosarcina barkeri (Q46E79), Methanosarcina barkeri Fusaro (Q46E79), Methanosarcina barkeri DSM 804 (Q46E79)
brenda
Cellitti, S.; Ou, W.; Chiu, H.; Gruenewald, J.; Jones, D.; Hao, X.; Fan, Q.; Quinn, L.; Ng, K.; Anfora, A.; Lesley, S.; Uno, T.; Brock, A.; Geierstanger, B.
D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine
Nat. Chem. Biol.
7
528-530
2011
Methanosarcina mazei (A0A4P8QYJ1)
brenda
Gaston, M.; Zhang, L.; Green-Church, K.; Krzycki, J.
The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine
Nature
471
647-650
2011
Methanosarcina acetivorans (Q8TUC0), Methanosarcina acetivorans ATCC 35395 (Q8TUC0), Methanosarcina acetivorans DSM 2834 (Q8TUC0), Methanosarcina acetivorans JCM 12185 (Q8TUC0)
brenda
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