5.1.1.1: alanine racemase
This is an abbreviated version!
For detailed information about alanine racemase, go to the full flat file.
Word Map on EC 5.1.1.1
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5.1.1.1
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pyridoxal
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5'-phosphate
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peptidoglycan
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racemization
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d-cycloserine
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stearothermophilus
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plp-dependent
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d-amino
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aldimine
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d-alanyl-d-alanine
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exosporium
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pyridoxal-5'-phosphate-dependent
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drug development
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5'-phosphate-dependent
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d-alanine:d-alanine
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medicine
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biotechnology
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pharmacology
- 5.1.1.1
- pyridoxal
- 5'-phosphate
- peptidoglycan
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racemization
- d-cycloserine
- stearothermophilus
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plp-dependent
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d-amino
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aldimine
- d-alanyl-d-alanine
- exosporium
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pyridoxal-5'-phosphate-dependent
- drug development
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5'-phosphate-dependent
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d-alanine:d-alanine
- medicine
- biotechnology
- pharmacology
Reaction
Synonyms
1SFT, AAR, alanine racemase, AlaR, ALR, alr-2, ALR1, ALR2, Alr2 racemase, AlrA, AlrAba, AlrBax, AlrMtb, alrTt, ARL, BA0252, BAS0238, CBL/ALR, CdAlr, cystathionine beta-lyase, D-alanine racemase, DadB, DadX, dadXOF4, dal1, EcAlr, EcCBL, EfAlaR, L-Alanine racemase, L-Alanine:D-alanine racemase, MBalr1, MBAlr2, MetC, More, MurI, OEOE_1641, PDB, Racemase, alanine, tAlaRac, TmCBL, wMelCBL
ECTree
5.1.1.1 alanine racemaseAdvanced search results
results (
results (Cofactor
Cofactor on EC 5.1.1.1 - alanine racemase
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COFACTOR 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
IMAGE
FAD
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not required as cofactor, slight activation at low concentrations, inhibition at high concentrations
pyridoxal 5'-phosphate
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the monomeric inactive enzyme appears to bind the cofactor pyridoxal 5'-phosphate by a non-covalent linkage, although the native dimeric enzyme binds the cofactor through an aldimine Schiff base linkage
pyridoxal 5'-phosphate
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not required as cofactor, slight activation at low concentrations, inhibition at high concentrations
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated
pyridoxal 5'-phosphate
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the sequence of 10 amino acid residues around the Lys residue, to which pyridoxal 5'-phosphate is bound, is identical with that of the dadB racemase
pyridoxal 5'-phosphate
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1 mol of pyridoxal 5'-phosphate is bound per subunit
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
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2 mol of pyridoxal 5'-phosphate bound per mol of enzyme dimer
pyridoxal 5'-phosphate
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2 mol of pyridoxal 5'-phosphate bound per mol of enzyme dimer
pyridoxal 5'-phosphate
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Arg219 forms a hydrogen bond with the pyridine nitrogen of the cofactor, Arg136 donates a hydrogen bond to the phenolic oxygen of pyridoxal 5'-phosphate and may be involved in the binding of substrate as well as stabilization of intermediates
pyridoxal 5'-phosphate
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Km: 0.000033 mM
pyridoxal 5'-phosphate
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contains one mol of pyridoxal 5'-phosphate per mol of enzyme
pyridoxal 5'-phosphate
dependent on
pyridoxal 5'-phosphate
both active sites of the dimer contain a pyridoxal 5'-phosphate molecule in aldimine linkage to Lys39 as a protonated Schiff base. The protonated pyridoxal 5'-phosphate-Lys39 Schiff base is the reactive form of the enzyme
pyridoxal 5'-phosphate
each monomer is comprised of two domains, an eight-stranded alpha/beta barrel containing the pyridoxal 5'-phosphate cofactor and a second domain primarily composed of beta-strands. The cofactor adopts two partially occupied conformational states that resemble previously reported and external aldimine complexes
pyridoxal 5'-phosphate
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enzyme is dependent on, maximal activity at 0.025 mM
pyridoxal 5'-phosphate
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Km at 30°C is 0.005 mM. Maximal activity is obtained in presence of more than 0.125 mM pyridoxal 5'-phosphate. The decrease in activity at incubation temperatures over 40°C is consistent with the decrease in the amount of bound pyridoxal 5'-phosphate
pyridoxal 5'-phosphate
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the pyridoxal form of the enzyme is converted to the pyridoxamine form by incubation with its natural substrate, D-alanine or L-alanine, under acidic conditions: the enzyme loses its racemase activity concomitantly. The pyridoxamine form of the enzyme returns to the pyridoxal form by incubation with pyruvate at alkaline pH
pyridoxal 5'-phosphate
Q81VF6
C-terminal region of 1 subdomain: Arg138 donates a hydrogen bond to the phenolic O atom of PLP, Arg224 donates a hydrogen bond to the pyridinyl N atom of PLP, Lys41 forms an aldimine linkage with the PLP, eliminating water to form the Schiff base, C-terminal atoms of second subunit Ser209, Gly226 and Ile227 stabilize the PLP phosphate with the help of Ser209 O(gamma), Tyr45 O(eta) and Tyr359 O(eta)
pyridoxal 5'-phosphate
once per 1 million turnovers of racemization a H-atom is added to C4-atom of the substrate moiety of the anionic intermediate instead of the reprotonation of the abstracted hydrogen at C(alpha) resulting in pyridoxamine 5'-phosphate
pyridoxal 5'-phosphate
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stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
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stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
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stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
Alkalihalophilus pseudofirmus
PLP is bound to the enzyme, adding PLP during developement of enzyme or to an assay is not necessary
pyridoxal 5'-phosphate
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PLP is inherently bound to the enzyme, removal of PLP inactivates the enzyme, adding PLP restores the activity, addition of 10 microM PLP to native enzyme slightly enhances activity
pyridoxal 5'-phosphate
dependent on, alanine racemase requires pyridoxal-5'-phosphate as a cofactor to form a Schiff base between pyridoxal 5'-phosphate and epsilon-amino group of the lysine residue in the active site
pyridoxal 5'-phosphate
dependent on, pyridoxal 5'-phosphate is bound to each monomer of the dimeric enzyme and forms a Schiff base with Lys39
pyridoxal 5'-phosphate
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PLP, dependent on
pyridoxal 5'-phosphate
PLP, dependent on, binding structure analysis: the phosphate group of the pyridoxal 5'-phosphate is stabilized by hydrogen bonds with the side chains of Tyr50, Ser222 and Tyr374, and with the backbone of Gly239, Ser222, and Ile240. The pyridine ring of the PLP is stabilized by a hydrogen bond between the N-1 of the cofactor and Nepsilon of Arg237. The C2A of the PLP also interacts with oxygen Q1 of the carboxylated Lys141. All residues stabilizing the PLP cofactor (Tyr50, Ser222, Gly239, Ile240, Arg237, Tyr374) are conserved among Alr proteins. But the AlrSco lacks one important hydrogen bond between Arg148 and the phenolic oxygen of the PLP molecule
pyridoxal 5'-phosphate
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PLP, dependent on, enzyme-cofactor complex structure, with inhibitor acetate, PDB ID 1SFT
pyridoxal 5'-phosphate
PLP, dependent on, no catalytic enzyme activity without, the apoenzyme activity is completely inhibited
pyridoxal 5'-phosphate
PLP, dependent on. The PLP-binding motif containing the catalytic Lys34 (sequence SMVKANAYGHG) is largely conserved between the various enzymes. The essential PLP cofactor is covalently bound to Lys34 via an internal aldimine linkage and extends towards the centre of the alpha/beta-barrel. The pyridine N1 of the PLP ring is stabilized by hydrogen bonding to Arg209, which is further stabilized by interactions with His159. The phosphate tail of PLP is stabilized by several residues from one monomer. The OP1 of the phosphate group hydrogen bonds to Ile212 and Tyr38, OP2 hydrogen bonds to Try341 and OP3 hydrogen bonds to Ile212 and Ser190. Arg132 is not within hydrogen-bonding distance of PLP in the AlrAba structure
pyridoxal 5'-phosphate
PLP, the PLP content of the enzyme is determined by a spectroscopic method
additional information
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exogenous pyridoxal 5-phosphate is not required, but enzyme may be pyridoxal 5-phosphate-dependent
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additional information
there is no additional density in the AlrAba structure consistent with the presence of any additional ligands besides pyridoxal 5'-phosphate
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additional information
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there is no additional density in the AlrAba structure consistent with the presence of any additional ligands besides pyridoxal 5'-phosphate
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