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Information on EC 4.1.1.90 - peptidyl-glutamate 4-carboxylase and Organism(s) Homo sapiens and UniProt Accession P38435

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     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.90 peptidyl-glutamate 4-carboxylase
IUBMB Comments
The enzyme can use various vitamin-K derivatives, including menaquinol, but does not contain iron. The mechanism appears to involve the generation of a strong base by oxygenation of vitamin K. It catalyses the post-translational carboxylation of glutamate residues of several proteins of the blood-clotting system. 9--12 glutamate residues are converted to 4-carboxyglutamate (Gla) in a specific domain of the target protein. The 4-pro-S hydrogen of the glutamate residue is removed and there is an inversion of stereochemistry at this position .
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Homo sapiens
UNIPROT: P38435
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
carboxylase, matrix gla protein, vitamin k-dependent carboxylase, gamma-glutamyl carboxylase, gamma-carboxylase, vitamin k-dependent gamma-glutamyl carboxylase, vkd carboxylase, gamma glutamyl carboxylase, vitamin k carboxylase, glutamate carboxylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylase
-
gamma-glutamyl carboxylase
glutamate carboxylase
-
matrix gamma-carboxyglutamate protein
-
matrix Gla protein
-
gamma glutamyl carboxylase
-
-
gamma-glutamyl carboxylase
-
-
glutamate carboxylase
-
-
two-chain carboxylase
-
carboxylase and epoxidase activities similar to those of one-chain carboxylase
vitamin K carboxylase
-
vitamin K-dependent carboxylase
-
-
vitamin K-dependent gamma-glutamyl carboxylase
-
-
VKD carboxylase
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylation
carboxylation
-
-
SYSTEMATIC NAME
IUBMB Comments
peptidyl-glutamate 4-carboxylase (2-methyl-3-phytyl-1,4-naphthoquinone-epoxidizing)
The enzyme can use various vitamin-K derivatives, including menaquinol, but does not contain iron. The mechanism appears to involve the generation of a strong base by oxygenation of vitamin K. It catalyses the post-translational carboxylation of glutamate residues of several proteins of the blood-clotting system. 9--12 glutamate residues are converted to 4-carboxyglutamate (Gla) in a specific domain of the target protein. The 4-pro-S hydrogen of the glutamate residue is removed [5] and there is an inversion of stereochemistry at this position [6].
CAS REGISTRY NUMBER
COMMENTARY hide
81181-72-8
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
FLEEL + CO2 + O2 + ammonium sulfate
? + vitamin K epoxide + H2O
show the reaction diagram
carboxylase activity is measured by 14CO2 incorporation into the synthetic peptide substrate FLEEL
-
-
?
FLEEL + CO2 + O2 + proFIX 19
? + vitamin K epoxide + H2O
show the reaction diagram
carboxylase activity is measured by 14CO2 incorporation into the synthetic peptide substrate FLEEL
-
-
?
FLEEL + CO2 + O2 + vitamin K hydroquinone
? + vitamin K epoxide + H2O
show the reaction diagram
-
-
-
?
FLEEL + CO2 + O2 + vitamin KH2
? + vitamin K epoxide + H2O
show the reaction diagram
carboxylase activity is measured by 14CO2 incorporation into the synthetic peptide substrate FLEEL
-
-
?
L-glutamate + CO2 + O2 + vitamin K hydroquinone
gamma-carboxy L-glutamate + vitamin K epoxide + H2O
show the reaction diagram
L-glutamate + CO2 + O2 + vitamin K hydroquinone
gamma-carboxy-L-glutamate + vitamin K epoxide + H2O
show the reaction diagram
reaction is essential for the activity of all of the vitamin K-dependent proteins
-
-
?
FLEEL + CO2 + O2 + proFIX 19
? + vitamin K epoxide + H2O
show the reaction diagram
-
-
-
-
?
FLEEL + CO2 + O2 + vitamin K hydroquinone
? + vitamin K epoxide + H2O
show the reaction diagram
-
pentapeptide substrate FLEEL: Phe-Leu-Glu-Glu-Leu, used for carboxylation activity
-
-
?
gamma-carboxylated glutamyl containing vitamin K-dependent protein + vitamin K epoxide + H2O
?
show the reaction diagram
-
-
-
-
?
glutamyl containing vitamin K-dependent protein + CO2 + vitamin K hydroquinone + O2
?
show the reaction diagram
-
propeptide binding increases carboxylase affinity for the Glu substrate, and the coordinated binding of the vitamin K–dependent propeptide and Glu substrate increase carboxylase affinity for vitamin K and activity, possibly through a mechanism of substrate-assisted catalysis. The propeptide adjacent to the Gla domain is cleaved subsequently to carboxylation. The carboxylase uses the energy of vitamin K hydroquinone oxygenation to convert glutamyl residues to gamma-carboxylated glutamyl residues in vitamin K–dependent proteins. During carboxylation, the vitamin K hydroquinone cofactor is oxidized to a vitamin K epoxide product. The carboxylase itself is also a vitamin K–dependent protein and carboxylase carboxylation may be important in regulating the overall process of vitamin K–dependent protein carboxylation. All vitamin K–dependent proteins contain multiple glutamyl residues that undergo carboxylation, which is accomplished by a processive mechanism. A single binding event between carboxylase and vitamin K–dependent protein can give rise to all of the glutamyl to gamm-carboxylated glutamyl conversions in the vitamin K–dependent protein. Carboxylation is limited to the glutamyl residue residing within the Gla domain
-
-
?
L-glutamate + CO2 + O2 + vitamin K hydroquinone
gamma-carboxy L-glutamate + vitamin K epoxide + H2O
show the reaction diagram
L-glutamate + CO2 + O2 + vitamin K hydroquinone
gamma-carboxy-L-glutamate + vitamin K epoxide + H2O
show the reaction diagram
-
-
-
-
?
osteocalcin + reduced vitamin K + CO2 + O2
carboxylated osteocalcin + vitamin K epoxide + H2O
show the reaction diagram
-
-
-
-
?
peptidyl-4-carboxyglutamate + 2,3-epoxyphylloquinone + H2O
peptidyl-glutamate + CO2 + O2 + phylloquinone
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-glutamate + CO2 + O2 + vitamin K hydroquinone
gamma-carboxy L-glutamate + vitamin K epoxide + H2O
show the reaction diagram
-
-
-
-
?
peptidyl-4-carboxyglutamate + 2,3-epoxyphylloquinone + H2O
peptidyl-glutamate + CO2 + O2 + phylloquinone
show the reaction diagram
-
-
-
-
?
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
vitamin K
vitamin K
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Boc-(2S,4S)-4-methylglutamic acid-Glu-Val
competitive inhibitor, FLEEL as substrate
warfarin
-
-
additional information
-
the carboxylase reaction is inhibited by sulfhydryl-specific reagents
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ammonium sulfate
-
proFIX 19
-
N-ethyl-2-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)hexadecylamide
-
2fold higher carboxylated osteocalcin synthesis in MG-63 cells in presence of the compound than with menaquinone-4. No cytotoxicity observed with concentrations up to 500 nM
N-ethyl-2-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)tetradecylamide
-
2.5fold higher carboxylated osteocalcin synthesis in MG-63 cells in presence of the compound than with menaquinone-4, No cytotoxicity observed with concentrations up to 500 nM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.54 - 24.3
FLEEL
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0019 - 0.21
FLEEL
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.013 - 2.1
Boc-(2S,4S)-4-methylglutamic acid-Glu-Val
additional information
additional information
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0000026
-
H160A mutant
0.0000027
-
wild type
0.0000045
-
H381A mutant
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 8.5
-
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
6-year-old Mexican American male
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
human glutamyl carboxylase spans the membrane at least 5times, with its N-terminus in the cytoplasm and its C-terminus in the lumen of the endoplasmic reticulum
Manually annotated by BRENDA team
amino-terminus of the gamma-glutamyl carboxylase is on the cytoplasmic side of the endoplasmic reticulum, while the carboxylterminus is on the lumenal side
Manually annotated by BRENDA team
758 residue integral membrane protein
Manually annotated by BRENDA team
microsomal carboxylase activity is compared from cells transfected with pCMV5
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
VKGC_HUMAN
758
5
87561
Swiss-Prot
other Location (Reliability: 3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60000
proteinase K digestion of the hGC-FLAG reveals a 60 kDa fragment, indicating the lumenal location of the FLAG tag and therefore the carboxyl-terminus of the carboxylase. In contrast, FLAG-hGC does not show a proteinase K–resistant fragment except for the residual undigested full-length carboxylase, which indicates the cytoplasmic location of the FLAG tag and therefore the amino-terminus of the carboxylase
87540
calculated from sequence
94000
SDS-PAGE
95000
full-length carboxylase
additional information
-
determination of disulfide bond formation in purified two-chain carboxylase and P80L and P378L two-chain carboxylases by SDS-PAGE and Western Blot analyses
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 94000, SDS-PAGE
heterodimer
-
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
-
-
additional information
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H404A
carboxylases W390A, S398A, and H404A have activities similar to that of wild type
L394R
natural mutant, certain individuals with combined deficiencies of vitamin K-dependent proteins have a mutation, L394R, in their gamma-glutamyl carboxylase causing impaired glutamate binding
S398A
carboxylases W390A, S398A, and H404A have activities similar to that of wild type
W390A
carboxylases W390A, S398A, and H404A have activities similar to that of wild type
W399A
lower activity than wild type
Y395A
lower activity than wild type
E373L/Q374L
-
transmembrane domain residues in the C-terminal peptide to test for polar/charge residues
G125L
-
two-chain carboxylase
G128L
-
two-chain carboxylase
G132L
-
two-chain carboxylase
G363L/T367L
-
transmembrane domain residues in the C-terminal peptide to test for polar/charge residues
H160A
-
His to Ala mutants all show full epoxidase activity
H287A
-
His to Ala mutants all show full epoxidase activity
H381A
-
His to Ala mutants all show full epoxidase activity
K218A
-
K218A activity is not detectable. The addition of exogenous amines restores K218A activity while having little effect on wild type carboxylase
L128R
-
warfarin resistent mutant
L368/372P
-
mutation to disrupt the transmembrane helix
P378L
-
significantly decreases the disulfide formation in carboxylase
P80L
-
mutation of residue P80, which has activity similar to that of wild-type carboxylase, has a minor effect on disulfide formation
R325Q
-
the mutation is associated with the bone mineral density
R58G
-
warfarin resistent mutant
V29L
-
warfarin resistent mutant
V45A
-
warfarin resistent mutant
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in 293 cells
expression of the cloned cDNA results in an increase in carboxylase activity in microsomes of transfected cells compared to mock-transfected cells
expressed in Sf9 cells
-
expression in Sf9 cell
-
mutational analysis is performed using an expression system lacking endogenous carboxylase. Construction of baculo viruses containing FLAG-tagged carboxylase mutants and expression in infected SF21 cells. Expresses the 758 amino acid human VKD carboxylase bearing a C-terminal extension of AAADYKDDDDK, where the last eight amino acids are the FLAG epitope
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
GGCX mRNA in the urolithiasic group is lower than that in the normal control group, which is on average 7.86fold underexpressed in the urolithiasic group compared to the normal control group. Protein expression of GGCX in the urolithiasic group is weaker than that in the control groups
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
six out of seven patients with Pseudoxanthoma Elasticum habor mutations in the GGCX gene (gamma-glutamyl carboxylase)
medicine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Rishavy, M.A.; Hallgren, K.W.; Yakubenko, A.V.; Shtofman, R.L.; Runge, K.W.; Berkner, K.L.
Bronsted analysis reveals Lys218 as the carboxylase active site base that deprotonates vitamin K hydroquinone to initiate vitamin K-dependent protein carboxylation
Biochemistry
45
13239-13248
2006
Homo sapiens
Manually annotated by BRENDA team
Berkner, K.L.
The vitamin K-dependent carboxylase
Annu. Rev. Nutr.
25
127-149
2005
Homo sapiens
Manually annotated by BRENDA team
Tie, J.K.; Zheng, M.Y.; Hsiao, K.L.; Perera, L.; Stafford, D.W.; Straight, D.L.
Transmembrane domain interactions and residue proline 378 are essential for proper structure, especially disulfide bond formation, in the human vitamin K-dependent gamma-glutamyl carboxylase
Biochemistry
47
6301-6310
2008
Homo sapiens
Manually annotated by BRENDA team
Tie, J.; Wu, S.; Jin, D.; Nicchitta, C.V.; Stafford, D.W.
A topological study of the human gamma-glutamyl carboxylase
Blood
96
973-978
2000
Homo sapiens (P38435), Homo sapiens
Manually annotated by BRENDA team
Mutucumarana, V.P.; Acher, F.; Straight, D.L.; Jin, D.Y.; Stafford, D.W.
A conserved region of human vitamin K-dependent carboxylase between residues 393 and 404 is important for its interaction with the glutamate substrate
J. Biol. Chem.
278
46488-46493
2003
Homo sapiens (P38435), Homo sapiens
Manually annotated by BRENDA team
Vanakker, O.M.; Martin, L.; Gheduzzi, D.; Leroy, B.P.; Loeys, B.L.; Guerci, V.I.; Matthys, D; Terry, S.F.; Coucke, P.J.; Pasquali-Ronchetti, I.; De Paepe, A.
Pseudoxanthoma elasticum-like phenotype with cutis laxa and multiple coagulation factor deficiency represents a separate genetic entity
J. Invest. Dermatol.
127
581-587
2007
Homo sapiens (P38435)
Manually annotated by BRENDA team
Crosier, M.D.; Peter, I.; Booth, S.L.; Bennett, G.; Dawson-Hughes, B.; Ordovas, J.M.
Association of sequence variations in vitamin K epoxide reductase and gamma-glutamyl carboxylase genes with biochemical measures of vitamin K status
J. Nutr. Sci. Vitaminol.
55
112-119
2009
Homo sapiens
Manually annotated by BRENDA team
Stafford, D.W.
The vitamin K cycle
J. Thromb. Haemost.
3
1873-1878
2005
Homo sapiens
Manually annotated by BRENDA team
Price, P.A.; Williamson, M.K.
Substrate recognition by the vitamin K-dependent gamma-glutamyl carboxylase: Identification of a sequence homology between the carboxylase and the carboxylase recognition site in the substrate
Protein Sci.
2
1987-1988
1993
Homo sapiens (P38435), Bos taurus (Q07175)
Manually annotated by BRENDA team
Wu, S.M.; Cheung, W.F.; Frazier, D.; Stafford, D.W.
Cloning and expression of the cDNA for human gamma-glutamyl carboxylase
Science
13
1634-1636
1991
Homo sapiens (P38435), Homo sapiens
Manually annotated by BRENDA team
Li, Q.; Schurgers, L.J.; Smith, A.C.; Tsokos, M.; Uitto, J.; Cowen, E.W.
Co-existent pseudoxanthoma elasticum and vitamin K-dependent coagulation factor deficiency: compound heterozygosity for mutations in the GGCX gene
Am. J. Pathol.
174
534-540
2009
Homo sapiens
Manually annotated by BRENDA team
Rai, A.J.; Udar, N.; Saad, R.; Fleisher, M.
A multiplex assay for detecting genetic variations in CYP2C9, VKORC1, and GGCX involved in warfarin metabolism
Clin. Chem.
55
823-826
2009
Homo sapiens
Manually annotated by BRENDA team
Qiao, J.; Wang, T.; Yang, J.; Liu, J.; Gong, X.; Guo, X.; Wang, S.; Ye, Z.
Genetic mutation of vitamin K-dependent gamma-glutamyl carboxylase domain in patients with calcium oxalate urolithiasis
J. Huazhong Univ. Sci. Technol. Med. Sci.
29
604-608
2009
Homo sapiens
Manually annotated by BRENDA team
Titapiwatanakun, R.; Rodriguez, V.; Middha, S.; Dukek, B.A.; Pruthi, R.K.
Novel splice site mutations in the gamma glutamyl carboxylase gene in a child with congenital combined deficiency of the vitamin K-dependent coagulation factors (VKCFD)
Pediatr. Blood Cancer
53
92-95
2009
Homo sapiens
Manually annotated by BRENDA team
Wang, T.; Yang, J.; Qiao, J.; Liu, J.; Guo, X.; Ye, Z.
Activity and expression of vitamin K-dependent gamma-glutamyl carboxylase in patients with calcium oxalate urolithiasis
Urol. Int.
85
94-99
2010
Homo sapiens
Manually annotated by BRENDA team
Rishavy, M.A.; Usubalieva, A.; Hallgren, K.W.; Berkner, K.L.
Novel insight into the mechanism of the vitamin K oxidoreductase (VKOR): electron relay through Cys43 and Cys51 reduces VKOR to allow vitamin K reduction and facilitation of vitamin K-dependent protein carboxylation
J. Biol. Chem.
286
7267-7278
2011
Homo sapiens
Manually annotated by BRENDA team
Wu, S.; Liu, S.; Davis, C.H.; Stafford, D.W.; Kulman, J.D.; Pedersen, L.G.
A hetero-dimer model for concerted action of vitamin K carboxylase and vitamin K reductase in vitamin K cycle
J. Theor. Biol.
279
143-149
2011
Homo sapiens (A7YA96)
Manually annotated by BRENDA team
King, C.R.; Deych, E.; Milligan, P.; Eby, C.; Lenzini, P.; Grice, G.; Porche-Sorbet, R.M.; Ridker, P.M.; Gage, B.F.
Gamma-glutamyl carboxylase and its influence on warfarin dose
Thromb. Haemost.
104
750-754
2010
Homo sapiens
Manually annotated by BRENDA team
Haraikawa, M.; Tsugawa, N.; Sogabe, N.; Tanabe, R.; Kawamura, Y.; Okano, T.; Hosoi, T.; Goseki-Sone, M.
Effects of gamma-glutamyl carboxylase gene polymorphism (R325Q) on the association between dietary vitamin K intake and gamma-carboxylation of osteocalcin in young adults
Asia Pac. J. Clin. Nutr.
22
646-654
2013
Homo sapiens
Manually annotated by BRENDA team
Parker, C.H.; Morgan, C.R.; Rand, K.D.; Engen, J.R.; Jorgenson, J.W.; Stafford, D.W.
A conformational investigation of propeptide binding to the integral membrane protein gamma-glutamyl carboxylase using nanodisc hydrogen exchange mass spectrometry
Biochemistry
53
1511-1520
2014
Homo sapiens
Manually annotated by BRENDA team
Vermeer, C.; van t Hoofd, C.; Knapen, M.H.J.; Xanthoulea, S.
Synthesis of 2-methyl-1,4-naphthoquinones with higher gamma-glutamyl carboxylase activity than MK-4 both in vitro and in vivo
Bioorg. Med. Chem. Lett.
27
208-211
2017
Homo sapiens, Rattus norvegicus
Manually annotated by BRENDA team