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Literature summary extracted from

  • Yoshida, A.; Tomita, T.; Atomi, H.; Kuzuyama, T.; Nishiyama, M.
    Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system (2016), J. Biol. Chem., 291, 21630-21643 .
    View publication on PubMedView publication on EuropePMC

Activating Compound

EC Number Activating Compound Comment Organism Structure
2.3.2.3 ADP 1 ADP is located in the active site of the enzyme Thermococcus kodakarensis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.2.1.106 expression in Escherichia coli Thermococcus kodakarensis
2.3.2.3 gene TK0278 or lysX, genetic organization of the lysine biosynthetic gene cluster, recombinant expression of His6-tagged and of untagged enzyme TkLysX in Escherichia coli strain BL21-CodonPlus (DE3)-RIL Thermococcus kodakarensis
2.6.1.124 the recombinant protein is produced in Escherichia coli BL21-CodonPlus (DE3)-RIL Thermococcus kodakarensis
6.3.2.43 expression in Escherichia coli Thermococcus kodakarensis
6.3.2.43 gene TK0278, recombinant expression of C-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21-CodonPlus (DE3)-RIL, recombinant expression of nontagged enzyme in Escherichia coli strain BL21(DE3) Thermococcus kodakarensis
6.3.2.60 gene TK0278, recombinant expression of C-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21-CodonPlus (DE3)-RIL, recombinant expression of nontagged enzyme in Escherichia coli strain BL21(DE3) Thermococcus kodakarensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.3.2.3 purified recombinant enzyme in complex with product LysW-gamma-AAA, hanging drop vapor diffusion method, method screening and subsequent optimization, mixing of 7.5 mg/ml enzyme, 2.5 mg/ml TkLysW, 10 mM AMP-PNP, 10 mM alpha-aminoadipate (AAA), or 50 mM glutamate, and 10 mM MgSO4 with crystallization solution containing 20% v/v 2-methyl-2,4-pentanediol, 6.6% w/v PEG 3350, 0.066 M imidazole, pH 6.5, and 0.132 M ammonium sulfate, 20°C, X-ray diffraction stucture determination and analysis at 2.18 A resolution Thermococcus kodakarensis
6.3.2.43 in presence of carrier protein LysW and AMP-PNP, MgSO4, and L-2-aminoadipate or glutamate, to 2.18 A resolution Thermococcus kodakarensis
6.3.2.43 purified recombinant nontagged enzyme TkLysX/ArgX in complex with [LysW]-C-terminal-N-(1,5-dicarboxypentan-1-yl)-L-glutamine ((TkLysX/ArgXx02LysW-gamma-AAA)), which corresponds to the structure of the post-reaction state of TkLysX/Arg, hanging drop vapor diffusion method, mixing of 7.5 mg/ml protein and 2.5 mg/ml TkLysW in 10 mM AMP-PNP, 10 mM AAA, or 50 mM glutamate and 10 mM MgSO4 with precipitation solution containing containing 20% v/v 2-methyl-2,4-pentanediol, 6.6% w/v PEG-3350, 0.066 M imidazole, pH 6.5, and 0.132 M ammonium sulfate, 20°C, X-ray diffraction structure determination and analysis at 2.18 A resolution. Molecular replacement. The asymmetric unit contains two TkLysX/ArgX tetramers, two intact TkLysW monomers each with one zinc atom, four partial TkLysW, eight ADP molecules, five phosphate ions, two sulfate ions, nine magnesium atoms, one free AAA molecule, and 628 water molecules. Good crystals containing TkLysW-gamma-Glu are not obtained Thermococcus kodakarensis
6.3.2.60 purified recombinant nontagged enzyme in complex with LysW and L-glutamate, good crystals containing TkLysW-gamma-Glu are not obtained Thermococcus kodakarensis

Protein Variants

EC Number Protein Variants Comment Organism
6.3.2.43 I185Y site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.43 additional information the N250G/A251F mutant is not produced as a soluble protein Thermococcus kodakarensis
6.3.2.43 N250G site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.43 S251F site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.43 Y175I site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.43 Y175I/I185Y/N250G/S251F mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.60 I185Y site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.60 additional information the N250G/A251F mutant is not produced as a soluble protein Thermococcus kodakarensis
6.3.2.60 N250G site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.60 S251F site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis
6.3.2.60 Y175I site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate Thermococcus kodakarensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.3.2.3 Mg2+ 2 magnesium atoms are located in the active site of the enzyme Thermococcus kodakarensis
2.3.2.3 phosphate 1 phosphate is located in the active site of the enzyme Thermococcus kodakarensis
6.3.2.43 Mg2+ required, nine Mg2+ ions per dimeric enzyme tetramer Thermococcus kodakarensis
6.3.2.43 additional information LysW contains a Zn2+ Thermococcus kodakarensis
6.3.2.60 Mg2+ required, two Mg2+ ions per enzyme molecule Thermococcus kodakarensis
6.3.2.60 additional information LysW contains a Zn2+ Thermococcus kodakarensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol Thermococcus kodakarensis
-
 tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol Thermococcus kodakarensis JCM 12380
-
 tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol Thermococcus kodakarensis ATCC BAA-918
-
 tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 additional information Thermococcus kodakarensis enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate ?
-
-
2.3.2.3 additional information Thermococcus kodakarensis JCM 12380 enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate ?
-
-
2.3.2.3 additional information Thermococcus kodakarensis ATCC BAA-918 enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate ?
-
-
2.6.1.124 an [amino-group carrier protein]-C-terminal-[gamma-(L-glutamate 5-semialdehyde-2-yl)-L-glutamate] + L-glutamate Thermococcus kodakarensis
-
 an [amino-group carrier protein]-C-terminal-[gamma-(L-ornithyl)-L-glutamate] + 2-oxoglutarate
-
 ?
3.5.1.132 [amino group carrier protein LysW]-C-terminal-gamma-(L-ornithyl)-L-glutamate + H2O Thermococcus kodakarensis
-
 [amino group carrier protein LysW]-C-terminal-L-glutamate + L-ornithine
-
 ?
6.3.2.43 ATP + an [amino group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate Thermococcus kodakarensis
-
 ADP + phosphate + an [amino group carrier protein]-C-terminal-N-(1,5-dicarboxypentan-1-yl)-L-glutamine
-
 ?
6.3.2.60 ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate Thermococcus kodakarensis
-
 ADP + phosphate + an [amino-group carrier protein]-C-terminal-gamma-(L-glutamyl)-L-glutamate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.2.1.106 Thermococcus kodakarensis Q5JFW1
-
-
1.2.1.106 Thermococcus kodakarensis ATCC BAA-918 Q5JFW1
-
-
2.3.2.3 Thermococcus kodakarensis Q5JFW0 i.e. Pyrococcus kodakaraensis strain KOD1
-
2.3.2.3 Thermococcus kodakarensis ATCC BAA-918 Q5JFW0 i.e. Pyrococcus kodakaraensis strain KOD1
-
2.3.2.3 Thermococcus kodakarensis JCM 12380 Q5JFW0 i.e. Pyrococcus kodakaraensis strain KOD1
-
2.6.1.124 Thermococcus kodakarensis Q5JFW3
-
-
3.5.1.132 Thermococcus kodakarensis
-
-
-
6.3.2.43 Thermococcus kodakarensis Q5JFW0
-
-
6.3.2.43 Thermococcus kodakarensis Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-
6.3.2.43 Thermococcus kodakarensis ATCC BAA-918 Q5JFW0
-
-
6.3.2.43 Thermococcus kodakarensis ATCC BAA-918 Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-
6.3.2.43 Thermococcus kodakarensis JCM 12380 Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-
6.3.2.60 Thermococcus kodakarensis Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-
6.3.2.60 Thermococcus kodakarensis ATCC BAA-918 Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-
6.3.2.60 Thermococcus kodakarensis JCM 12380 Q5JFW0 Pyrococcus kodakaraensis strain KOD1
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.3.2.3 recombinant His6-tagged and of untagged enzyme TkLysX from Escherichia coli strain BL21-CodonPlus (DE3)-RIL, recombinant His6-tagged enzyme by nickel affinity chromatography, recombinant untagged enzyme by ammonium sulfate fractionation, hydrophobic interaction chromatography, ultrafiltration, anion exchange chromatography, gel filtration, and ultrafiltration Thermococcus kodakarensis
6.3.2.43 recombinant C-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21-CodonPlus (DE3)-RIL by heat treatment at 80°C for 20 min and nickel affinity chromatography. Recombinant nontagged enzyme from Escherichia coli strain BL21(DE3) by heat treatment at 80°C for 20 min, ammonium sulfate fractionation, hydrophobic interaction chromatography, ultrafiltration, and gel filtration Thermococcus kodakarensis
6.3.2.60 recombinant C-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21-CodonPlus (DE3)-RIL by heat treatment at 80°C for 20 min and nickel affinity chromatography. Recombinant nontagged enzyme from Escherichia coli strain BL21(DE3) by heat treatment at 80°C for 20 min, ammonium sulfate fractionation, hydrophobic interaction chromatography, ultrafiltration, and gel filtration Thermococcus kodakarensis

Reaction

EC Number Reaction Comment Organism Reaction ID
6.3.2.43 ATP + an [amino group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + an [amino group carrier protein]-C-terminal-N-(1,4-dicarboxybutyl)-L-glutamine substrate-recognition mechanism of bifunctional TkLysX/ArgX Thermococcus kodakarensis
a
6.3.2.60 ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate = ADP + phosphate + an [amino-group carrier protein]-C-terminal-gamma-(L-glutamyl)-L-glutamate substrate-recognition mechanism of bifunctional TkLysX/ArgX Thermococcus kodakarensis
a

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
6.3.2.43 0.016
-
 substrate L-glutamate, pH not specified in the publication, temperature not specified in the publication Thermococcus kodakarensis
6.3.2.43 0.021
-
 substrate L-2-aminoadipate, pH not specified in the publication, temperature not specified in the publication Thermococcus kodakarensis
6.3.2.43 0.021
-
 pH 8.0, 60°C, recombinant enzyme Thermococcus kodakarensis
6.3.2.60 0.016
-
 pH 8.0, 60°C, recombinant enzyme Thermococcus kodakarensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.2.1.106 [amino-group carrier protein LysW]-C-terminal-gamma-(alpha-aminoadipate) phosphate + NADPH + H+
-
 Thermococcus kodakarensis [amino-group carrier protein LysW]-C-terminal-gamma-aminoadipic semialdehyde + phosphate + NADP+
-
 r
1.2.1.106 [amino-group carrier protein LysW]-C-terminal-gamma-(alpha-aminoadipate) phosphate + NADPH + H+
-
 Thermococcus kodakarensis ATCC BAA-918 [amino-group carrier protein LysW]-C-terminal-gamma-aminoadipic semialdehyde + phosphate + NADP+
-
 r
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol
-
 Thermococcus kodakarensis tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol
-
 Thermococcus kodakarensis JCM 12380 tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 L-lysyl-tRNALys + phosphatidylglycerol
-
 Thermococcus kodakarensis ATCC BAA-918 tRNALys + 3-O-L-lysyl-1-O-phosphatidylglycerol
-
 ?
2.3.2.3 additional information enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate Thermococcus kodakarensis ?
-
-
2.3.2.3 additional information the enzyme LysX also forms LysW-gamma-(alpha-aminoadipate) (LysW-gamma-AAA) from alpha-amino adipate (AAA) and glutamate as substrates and ligates both compounds with TK0279, the amino group carrier protein LysW in this microorganism, in an ATP-dependent manner. LysX, forming an isopeptide bond between the alpha-amino group of AAA and gamma-carboxyl group of the glutamate residue at the C terminus of LysW Thermococcus kodakarensis ?
-
-
2.3.2.3 additional information enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate Thermococcus kodakarensis JCM 12380 ?
-
-
2.3.2.3 additional information the enzyme LysX also forms LysW-gamma-(alpha-aminoadipate) (LysW-gamma-AAA) from alpha-amino adipate (AAA) and glutamate as substrates and ligates both compounds with TK0279, the amino group carrier protein LysW in this microorganism, in an ATP-dependent manner. LysX, forming an isopeptide bond between the alpha-amino group of AAA and gamma-carboxyl group of the glutamate residue at the C terminus of LysW Thermococcus kodakarensis JCM 12380 ?
-
-
2.3.2.3 additional information enzyme LysX from Thermococcus kodakarensis catalyzes the conjugation of enzyme LysW with either alpha-aminoadipate (AAA) or glutamate Thermococcus kodakarensis ATCC BAA-918 ?
-
-
2.3.2.3 additional information the enzyme LysX also forms LysW-gamma-(alpha-aminoadipate) (LysW-gamma-AAA) from alpha-amino adipate (AAA) and glutamate as substrates and ligates both compounds with TK0279, the amino group carrier protein LysW in this microorganism, in an ATP-dependent manner. LysX, forming an isopeptide bond between the alpha-amino group of AAA and gamma-carboxyl group of the glutamate residue at the C terminus of LysW Thermococcus kodakarensis ATCC BAA-918 ?
-
-
2.6.1.124 an [amino-group carrier protein]-C-terminal-[gamma-(L-glutamate 5-semialdehyde-2-yl)-L-glutamate] + L-glutamate
-
 Thermococcus kodakarensis an [amino-group carrier protein]-C-terminal-[gamma-(L-ornithyl)-L-glutamate] + 2-oxoglutarate
-
 ?
3.5.1.132 [amino group carrier protein LysW]-C-terminal-gamma-(L-ornithyl)-L-glutamate + H2O
-
 Thermococcus kodakarensis [amino group carrier protein LysW]-C-terminal-L-glutamate + L-ornithine
-
 ?
6.3.2.43 ATP + an [amino group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis ADP + phosphate + an [amino group carrier protein]-C-terminal-N-(1,5-dicarboxypentan-1-yl)-L-glutamine
-
 ?
6.3.2.43 ATP + an [amino group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate the amino-group carrier protein is LysW. Determination of the crystal structure of the LysX family protein from Thermococcus kodakarensis, which catalyzes the conjugation of LysW with either alpha-aminoadipate (AAA) or glutamate, in a complex with LysW-gamma-AAA. Substrate binding structure, overview. Residues Thr196, Asn250, and Ala251 are involved in the recognition of the delta-carboxyl group of AAA Thermococcus kodakarensis ADP + phosphate + an [amino group carrier protein]-C-terminal-N-(1,5-dicarboxypentan-1-yl)-L-glutamine
-
 ?
6.3.2.43 ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-2-aminoadip-2-yl)-L-glutamate
-
 ?
6.3.2.43 ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis JCM 12380 ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-2-aminoadip-2-yl)-L-glutamate
-
 ?
6.3.2.43 ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis ATCC BAA-918 ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-2-aminoadip-2-yl)-L-glutamate
-
 ?
6.3.2.43 ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-glutamate
-
 Thermococcus kodakarensis ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-glutam-2-yl)-L-glutamate
-
 ?
6.3.2.43 ATP + [LysW mutant E42R]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis ADP + phosphate + [LysW mutant E42R]-C-terminal-N-(1,5-dicarboxypentan-1-yl)-L-glutamine
-
 ?
6.3.2.43 ATP + [LysW]-C-terminal-L-glutamate + L-2-aminoadipate
-
 Thermococcus kodakarensis ADP + phosphate + [LysW]-C-terminal-N-(1,4-dicarboxybutan-1-yl)-L-glutamine
-
 ?
6.3.2.43 additional information purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner Thermococcus kodakarensis ?
-
-
6.3.2.43 additional information purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner Thermococcus kodakarensis JCM 12380 ?
-
-
6.3.2.43 additional information purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner Thermococcus kodakarensis ATCC BAA-918 ?
-
-
6.3.2.60 ATP + L-glutamate + an [amino-group carrier protein mutant E42R]-C-terminal-L-glutamate
-
 Thermococcus kodakarensis ADP + phosphate + an [amino-group carrier protein mutant E42R]-C-terminal-gamma-(L-glutamyl)-L-glutamate
-
 ?
6.3.2.60 ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate
-
 Thermococcus kodakarensis ADP + phosphate + an [amino-group carrier protein]-C-terminal-gamma-(L-glutamyl)-L-glutamate
-
 ?
6.3.2.60 ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate the amino-group carrier protein is LysW. Determination of the crystal structure of the LysX family protein from Thermococcus kodakarensis, which catalyzes the conjugation of LysW with either alpha-aminoadipate (AAA) or glutamate, in a complex with LysW-gamma-AAA. Residue Tyr175 in TkLysX/ArgX plays a critical role in the recognition of glutamate Thermococcus kodakarensis ADP + phosphate + an [amino-group carrier protein]-C-terminal-gamma-(L-glutamyl)-L-glutamate
-
 ?
6.3.2.60 additional information purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner Thermococcus kodakarensis ?
-
-

Subunits

EC Number Subunits Comment Organism
2.3.2.3 tetramer crystal structure analysis Thermococcus kodakarensis
6.3.2.43 tetramer the crystal asymmetric unit contains two TkLysX/ArgX tetramers, two intact TkLysW monomers each with one zinc atom, four partial TkLysW, eight ADP molecules, five phosphate ions, two sulfate ions, nine magnesium atoms, one free AAA molecule, and 628 water molecules, binding structure, overview Thermococcus kodakarensis
6.3.2.60 tetramer the crystal asymmetric unit contains two TkLysX/ArgX tetramers, two intact TkLysW monomers each with one zinc atom, four partial TkLysW, eight ADP molecules, five phosphate ions, two sulfate ions, nine magnesium atoms, one free AAA molecule, and 628 water molecules, binding structure, overview Thermococcus kodakarensis

Synonyms

EC Number Synonyms Comment Organism
1.2.1.106 lysY
-
 Thermococcus kodakarensis
1.2.1.106 TK0277
-
 Thermococcus kodakarensis
1.2.1.106 [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase
-
 Thermococcus kodakarensis
2.3.2.3 LysX
-
 Thermococcus kodakarensis
2.3.2.3 RimK-related lysine biosynthesis protein UniProt Thermococcus kodakarensis
2.3.2.3 Tk0278
-
 Thermococcus kodakarensis
2.3.2.3 TkLysX
-
 Thermococcus kodakarensis
2.6.1.124 lysJ
-
 Thermococcus kodakarensis
3.5.1.132 lysK
-
 Thermococcus kodakarensis
3.5.1.132 TK0274
-
 Thermococcus kodakarensis
6.3.2.43 LysX
-
 Thermococcus kodakarensis
6.3.2.43 More cf. EC 6.3.2.60 Thermococcus kodakarensis
6.3.2.43 RimK-related lysine biosynthesis protein UniProt Thermococcus kodakarensis
6.3.2.43 Tk0278
-
 Thermococcus kodakarensis
6.3.2.43 TkLysX/ArgX
-
 Thermococcus kodakarensis
6.3.2.60 ArgX
-
 Thermococcus kodakarensis
6.3.2.60 More cf. EC 6.3.2.43 Thermococcus kodakarensis
6.3.2.60 RimK-related lysine biosynthesis protein UniProt Thermococcus kodakarensis
6.3.2.60 Tk0278
-
 Thermococcus kodakarensis
6.3.2.60 TkLysX/ArgX
-
 Thermococcus kodakarensis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
6.3.2.43 60
-
 assay at Thermococcus kodakarensis
6.3.2.60 60
-
 assay at Thermococcus kodakarensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.43 8
-
 assay at Thermococcus kodakarensis
6.3.2.60 8
-
 assay at Thermococcus kodakarensis

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.43 ATP
-
 Thermococcus kodakarensis
6.3.2.60 ATP
-
 Thermococcus kodakarensis

General Information

EC Number General Information Comment Organism
2.3.2.3 evolution the enzyme belongs to the LysX family of enzymes. Analysis of the mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities, overview. Substrate recognition mechanism in LysX family proteins. The lysX homologues in the lysine biosynthetic gene cluster encode enzymes that possess the signature motif (Tyr175, Ile185, Thr196, and Asn250-Ala251) for the LysX/ArgX bifunctional enzyme Thermococcus kodakarensis
2.3.2.3 metabolism the enzyme LysX is involved in the lysine biosynthesis pathway. The conversion from alpha-aminoadipate (AAA) to lysine, is accomplished by five enzymes: LysX, LysZ, LysY, LysJ, and LysK, using the amino group carrier protein LysW. The alpha-amino group of AAA is modified with LysW by LysX, forming an isopeptide bond between the alpha-amino group of AAA and gamma-carboxyl group of the glutamate residue at the C terminus of LysW. LysW-gamma-AAA thus synthesized is then transferred to subsequent biosynthetic enzymes to be converted to LysW-gamma-lysine by phosphorylation, reduction, and amination steps. In the final step, LysW-gamma-lysine is recognized by LysK, a carboxypeptidase, resulting in the release of lysine. LysW contains many acidic amino acid residues for electrostatic interactions with each enzyme, and, thus, functions as an amino group carrier protein for efficient lysine biosynthesis Thermococcus kodakarensis
2.3.2.3 additional information crystal structure analysis revealing the mechanism of substrate recognition of alpha-aminoadipate substrate by LysX and structural basis for the bifunctionality of the LysX family protein from Thermococcus kodakarensis Active site structure and reaction mechanism, structure-function analysis, detailed overview. ADP, a phosphate ion, two magnesium atoms, and the C-terminus of TkLysW-gamma-AAA are located in the active site of TkLysX Thermococcus kodakarensis
2.6.1.124 physiological function the enzyme participates in an L-arginine biosynthetic pathway Thermococcus kodakarensis
6.3.2.43 evolution proposal of a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities Thermococcus kodakarensis
6.3.2.43 metabolism the enzyme is part of the lysine biosynthetic pathway in Thermococcus kodakarensis, overview. The gene cluster for lysine biosynthetic genes through AAA produces lysine with a LysW-mediated system. In this cluster, TK0279, TK0278, TK0276, TK0277, TK0275, and TK0274 are expected to be responsible for the conversion process from AAA to lysine through the LysW system as LysW-gamma-AAA synthetase, LysW-gamma-AAA kinase, LysW-gamma-AAA semialdehyde dehydrogenase, LysW-gamma-lysine aminotransferase, and LysW-gamma-lysine carboxypeptidase, respectively. LysW-gamma-AAA thus synthesized is transferred to subsequent biosynthetic enzymes to be converted to LysW-gamma-lysine by phosphorylation, reduction, and amination steps. In the final step, LysW-gamma-lysine is recognized by LysK, a carboxypeptidase, resulting in the release of lysine. The lysine biosynthetic enzymes of Thermococcus kodakarensis convert AAA/Glu to lysine/ornithine Thermococcus kodakarensis
6.3.2.43 additional information the modification by TK0278 and successive phosphorylation by TK0276 occurr at the C-terminus of TkLysW. Residue Tyr175 in TkLysX/ArgX plays a critical role in the recognition of glutamate. Residues Thr196, Asn250, and Ala251 are involved in the recognition of the delta-carboxyl group of AAA. The Tyr residue at strand beta10, the Tyr residue at strand beta11, and the Thr residue at the large loop as the additional key residues that define substrate specificity in LysX family proteins Thermococcus kodakarensis
6.3.2.43 physiological function Thermococcus kodakarensis has the potential to biosynthesize lysine and ornithine using the carrier protein LysW-mediated system with a single set of bifunctional enzymes Thermococcus kodakarensis
6.3.2.43 physiological function enzyme LysX recognizes alpha-aminoadipate (AAA) as a substrate, structural basis for the bifunctionality of the LysX family protein from Thermococcus kodakarensis. Purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner. Proposal of a mechanism for substrate recognition Thermococcus kodakarensis
6.3.2.60 evolution proposal of a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities Thermococcus kodakarensis
6.3.2.60 malfunction enzyme mutants Y175I, I185Y, N250G, and S251F exhibit an apparent substrate preference for glutamate, suggesting that Tyr at 185 compensates for the function of Tyr175 in the recognition of the gamma-carboxyl group of glutamate Thermococcus kodakarensis
6.3.2.60 metabolism the enzyme is part of the lysine biosynthetic pathway in Thermococcus kodakarensis, overview. The lysine biosynthetic enzymes of Thermococcus kodakarensis convert AAA/Glu to lysine/ornithine Thermococcus kodakarensis
6.3.2.60 additional information the modification by TK0278 and successive phosphorylation by TK0276 occurr at the C terminus of TkLysW. Residue Tyr175 in TkLysX/ArgX plays a critical role in the recognition of glutamate. Residues Thr196, Asn250, and Ala251 are involved in the recognition of the delta-carboxyl group of AAA. The Tyr residue at strand beta10, the Tyr residue at strand beta11, and the Thr residue at the large loop as the additional key residues that define substrate specificity in LysX family proteins Thermococcus kodakarensis
6.3.2.60 physiological function purified recombinant TK0278 recognizes alpha-aminoadipate (AAA) and glutamate as substrates and ligated both compounds with TK0279, an amino group carrier protein LysW in this microorganism, in an ATP-dependent manner. Proposal of a mechanism for substrate recognition Thermococcus kodakarensis