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Information on EC 6.3.2.60 - glutamate---[amino group carrier protein] ligase
for references in articles please use BRENDA:EC6.3.2.60
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EC Tree 6 Ligases
6.3 Forming carbon-nitrogen bonds
6.3.2 Acid—amino-acid ligases (peptide synthases)
6.3.2.60 glutamate---[amino group carrier protein] ligase
IUBMB Comments
The enzyme, originally characterized from the archaeon Sulfolobus acidocaldarius, is involved in L-arginine biosynthesis. The enzyme from the archaeon Thermococcus kodakarensis is bifunctional and also catalyses the activity of EC 6.3.2.43, [amino-group carrier protein]—L-2-aminoadipate ligase.
The enzyme appears in viruses and cellular organisms
Reaction Schemes
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an [amino-group carrier protein]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Synonyms
ArgX, More, RimK-related lysine biosynthesis protein, StArgX, Tk0278, TkLysX/ArgX, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ArgX
StArgX
additional information
ArgX
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
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
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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
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
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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
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SYSTEMATIC NAME
IUBMB Comments
L-glutamate:an [amino-group carrier protein]-C-terminal-L-glutamate ligase (ADP-forming)
The enzyme, originally characterized from the archaeon Sulfolobus acidocaldarius, is involved in L-arginine biosynthesis. The enzyme from the archaeon Thermococcus kodakarensis is bifunctional and also catalyses the activity of EC 6.3.2.43, [amino-group carrier protein]---L-2-aminoadipate ligase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + L-glutamate + an [amino-group carrier protein mutant E42R]-C-terminal-L-glutamate
ADP + phosphate + an [amino-group carrier protein mutant E42R]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
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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
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
additional information
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Substrates: 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
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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
Substrates: -
Products: -
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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
Substrates: 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
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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
Substrates: -
Products: -
Products: -
?
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
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ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
Products: -
?
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
Products: -
?
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
Products: -
?
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
Products: -
?
ATP + L-glutamate + [LysW]-C-terminal-L-glutamate
ADP + phosphate + [LysW]-C-terminal-gamma-(L-glutamyl)-L-glutamate
Substrates: -
Products: -
Products: -
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
sulfate
enzyme bound, the sulfate ion is replaced with the phosphate moiety of acylphosphate intermediate of StLysW in the structure model
additional information
additional information
LysW contains an N-terminally bound Zn2+
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Pyrococcus kodakaraensis strain KOD1
UniProt
brenda
Pyrococcus kodakaraensis strain KOD1
UniProt
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
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
metabolism
physiological function
additional information
evolution
gene duplication events at different stages of evolution led to ArgX and LysX (EC 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
evolution
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gene duplication events at different stages of evolution led to ArgX and LysX (EC 6.3.2.43)
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evolution
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gene duplication events at different stages of evolution led to ArgX and LysX (EC 6.3.2.43)
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evolution
-
gene duplication events at different stages of evolution led to ArgX and LysX (EC 6.3.2.43)
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evolution
-
gene duplication events at different stages of evolution led to ArgX and LysX (EC 6.3.2.43)
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evolution
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gene duplication events at different stages of evolution led to ArgX and LysX (EC 6.3.2.43)
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metabolism
lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
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
metabolism
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lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
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metabolism
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lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
-
metabolism
-
lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
-
metabolism
-
lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
-
metabolism
-
lysine and arginine biosyntheses are mediated by a common carrier protein in Sulfolobus acidocaldarius. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions
-
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
physiological function
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
physiological function
-
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
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physiological function
-
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
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physiological function
-
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
-
physiological function
-
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
-
physiological function
-
the hyperthermophilic archaeon Sulfolobus acidocaldarius not only biosynthesizes lysine through LysW-mediated protection of alpha-aminoadipate (AAA), but also uses the amino-group carrier protein LysW to protect the amino group of glutamate in arginine biosynthesis, cf. EC 6.3.2.43. ArgX is the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW
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additional information
StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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
additional information
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StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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additional information
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StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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additional information
-
StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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additional information
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StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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additional information
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StArgX/ADP structrue analysis, and structure of substrate StLysW and recognition by enzyme StArgX, structural model of the phosphoryl intermediate in the StArgX reaction, overview. The alpha-amino group of the substrate glutmate molecule is to be ligated with the gamma-carboxyl group of Glu56 residue of StLysW. Interaction analysis of ArgX and LysW
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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). ARGX_SULAC
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
282
0
31715
Swiss-Prot
-
Q5JFW0_THEKO
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
273
0
30488
TrEMBL
-
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
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
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
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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
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme in complex with ADP and with substrate StLysW, X-ray diffraction structure determination and analysis at 1.8 A resolution
purified recombinant nontagged enzyme in complex with LysW and L-glutamate, good crystals containing TkLysW-gamma-Glu are not obtained
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
I185Y
site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate
N250G
site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate
S251F
site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate
Y175I
site-directed mutagenesis, the mutant exhibits an apparent substrate preference for glutamate
additional information
the N250G/A251F mutant is not produced as a soluble protein
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
J. Biol. Chem.
291
21630-21643
2016
Thermococcus kodakarensis (Q5JFW0), Thermococcus kodakarensis JCM 12380 (Q5JFW0), Thermococcus kodakarensis ATCC BAA-918 (Q5JFW0)
brenda
Ouchi, T.; Tomita, T.; Horie, A.; Yoshida, A.; Takahashi, K.; Nishida, H.; Lassak, K.; Taka, H.; Mineki, R.; Fujimura, T.; Kosono, S.; Nishiyama, C.; Masui, R.; Kuramitsu, S.; Albers, S.V.; Kuzuyama, T.; Nishiyama, M.
Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus
Nat. Chem. Biol.
9
277-283
2013
Sulfolobus acidocaldarius (Q4J8E7), Sulfolobus acidocaldarius DSM 639 (Q4J8E7), Sulfolobus acidocaldarius ATCC 33909 (Q4J8E7), Sulfolobus acidocaldarius NBRC 15157 (Q4J8E7), Sulfolobus acidocaldarius NCIMB 11770 (Q4J8E7), Sulfolobus acidocaldarius JCM 8929 (Q4J8E7)
brenda
EXTERNAL LINKS (specific for EC-Number 6.3.2.60)
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Release 2023.1 (January 2023)
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