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Information on EC 5.1.1.3 - glutamate racemase and Organism(s) Aquifex pyrophilus and UniProt Accession P56868

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EC Tree
     5 Isomerases
         5.1 Racemases and epimerases
             5.1.1 Acting on amino acids and derivatives
                5.1.1.3 glutamate racemase
IUBMB Comments
A pyridoxal-phosphate protein.
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This record set is specific for:
Aquifex pyrophilus
UNIPROT: P56868
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Word Map
The taxonomic range for the selected organisms is: Aquifex pyrophilus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
glutamate racemase, race2, race1, d-glutamate racemase, glutamic acid racemases, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glutamate racemase
-
glutamate racemase
-
-
Racemase, glutamate
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-glutamate = D-glutamate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
racemization
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
glutamate racemase
A pyridoxal-phosphate protein.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-08-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-glutamate
L-glutamate
show the reaction diagram
-
-
-
?
L-glutamate
D-glutamate
show the reaction diagram
L-glutamate
D-glutamate
show the reaction diagram
-
-
-
-
?
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
D-glutamate
show the reaction diagram
the enzyme is responsible for the synthesis of D-glutamate, an essential building block of the peptidoglycan layer in bacterial cell walls
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-Gln
competitive
additional information
-
the pressure does not affect catalysis after substrate binding
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
the pressure does not affect catalysis after substrate binding
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21 - 3
D-glutamate
3.2 - 11
L-glutamate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00034 - 3.3
D-glutamate
0.0023 - 0.21
L-glutamate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
computer simulations on a QM/MM (quantum mechanics/molecular mechanics) potential energy surface are carried out to gain insights into the catalytic mechanism of glutamate racemase (MurI). Results suggest at least two possible roles for MurI as a catalyst: (1) to activate the bound substrate by donating a proton to its carboxylate main chain in a step prior to the racemization process and (2) to optimize the differential stabilization of the intermediate relative to the reactant via an intermolecular effect that comes, partly, from a desolvation effect on the reactant in going from water to the enzyme environment and, partly, from a stabilization effect on the intermediate by the enzymatic residues. Thus, the catalytic effect of glutamate racemase is achieved without resorting to covalent bond formation between the enzyme or cofactor and the transition state.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
MURI_AQUPY
254
0
27993
Swiss-Prot
-
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
each monomer consists of two alpha/beta fold domains
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, crystal structure of apo-enzyme and enzyme complexed with a substrate analog, D-glutamine, by multiwavelength anomalous dispersion method using a thimerosal-bound MurI crystal, determined at 2.3 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D7S
turnover number is decreased by 170fold compared to wild-type enzyme in the D to L reaction, it is decreased by about 6fold compared to wild-type enzyme in the L to D reaction
E147N
turnover number is decreased by 100fold compared to wild-type enzyme in the D to L reaction, it is decreased by about 7fold compared to wild-type enzyme in the L to D reaction
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lee, K.S.; Chi, Y.M.; Yu, Y.G.
Effect of pressure on catalytic properties of glutamate racemase from Aquifex pyrophilus, an extremophilic bacteria
J. Microbiol. Biotechnol.
12
149-152
2002
Aquifex pyrophilus
-
Manually annotated by BRENDA team
Hwang, K.Y.; Cho, C.S.; Kim, S.S.; Sung, H.C.; Yu, Y.G.; Cho, Y.
Structure and mechanism of glutamate racemase from Aquifex pyrophilus
Nat. Struct. Biol.
6
422-426
1999
Aquifex pyrophilus (P56868), Aquifex pyrophilus
Manually annotated by BRENDA team
Mobitz, H.; Bruice, T.C.
Multiple substrate binding states and chiral recognition in cofactor-independent glutamate racemase: a molecular dynamics study
Biochemistry
43
9685-9694
2004
Aquifex pyrophilus (P56868), Aquifex pyrophilus
Manually annotated by BRENDA team
Puig, E.; Garcia-Viloca, M.; Gonzalez-Lafont, A.; Lluch, J.M.
On the ionization state of the substrate in the active site of glutamate racemase. A QM/MM study about the importance of being zwitterionic
J. Phys. Chem. A
110
717-725
2006
Aquifex pyrophilus
Manually annotated by BRENDA team
Puig, E.; Garcia-Viloca, M.; Gonzalez-Lafont, A.; Lluch, J.M.; Field, M.J.
New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations
J. Phys. Chem. B
111
2385-2397
2007
Aquifex pyrophilus (P56868)
Manually annotated by BRENDA team
Okrasa, K.; Levy, C.; Hauer, B.; Baudendistel, N.; Leys, D.; Micklefield, J.
Structure and mechanism of an unusual malonate decarboxylase and related racemases
Chem. Eur. J.
14
6609-6613
2008
Aquifex pyrophilus (P56868)
Manually annotated by BRENDA team