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Literature summary extracted from
- Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system (2014), Nat. Commun., 5, 3615 .
Activating Compound
| EC Number | Activating Compound | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.2.1 | additional information | lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Effect of accessory Lar proteins and cofactors on the in vitro activation of LarANiDELTABCE (apo-LarA) by LarENiBC, overview. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation | Lactiplantibacillus plantarum |
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 4.99.1.12 | expressed in Lactococcus lactis | Lactiplantibacillus plantarum |
| 5.1.2.1 | gene larA, encoded in the lar operon, clustering of lar genes and genotyping, overview. Recombinant expression of N- or C-terminally StrepII-tagged LarA in Lactobacillus lactis | Lactiplantibacillus plantarum |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 5.1.2.1 | purified enzyme, free or Hg-labeled, hanging drop vapour diffusion method, mixing of 0.002 ml of 16 mg/ml protein solution with 0.002 ml of reservoir solution containing 22% PEG monomethyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 0.2 M sodium malonate pH 7.0 and 0.02% w/v sodium azide, at 18°C, a few days, X-ray diffraction structure determination and analysis at 1.8-2.0 A resolution | Lactiplantibacillus plantarum |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.2.1 | 11 | - |
(R)-lactate | pH and temperature not specified in the publication | Lactiplantibacillus plantarum |  |
| 5.1.2.1 | 46 | - |
(S)-lactate | pH and temperature not specified in the publication | Lactiplantibacillus plantarum | |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 4.99.1.12 | Ni2+ | contains Ni2+ | Lactiplantibacillus plantarum | |
| 5.1.2.1 | additional information | model of the assembly of the lactate racemase metallocenter, overview. Enzyme LarA receives Ni2+ from the pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase, LarE (EC 4.4.1.37) | Lactiplantibacillus plantarum | |
| 5.1.2.1 | Ni2+ | dependent on, nickel is an essential cofactor, the enzyme contains 19-21% nickel, measured by PAR assays and ICP-AES. The LarA Ni center is coordinated by His residues, a four coordinate square planar nickel center or a five coordinate square pyramidal site | Lactiplantibacillus plantarum | |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.99.1.12 | Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide | Lactiplantibacillus plantarum | - |
pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni2+ | - |
? | |
| 4.99.1.12 | Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide | Lactiplantibacillus plantarum NCIMB 8826 | - |
pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni2+ | - |
? | |
| 5.1.2.1 | (S)-lactate | Lactiplantibacillus plantarum | - |
(R)-lactate | - |
r | |
| 5.1.2.1 | (S)-lactate | Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1 | - |
(R)-lactate | - |
r | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 4.99.1.12 | Lactiplantibacillus plantarum | F9UST1 | - |
- |
| 4.99.1.12 | Lactiplantibacillus plantarum NCIMB 8826 | F9UST1 | - |
- |
| 5.1.2.1 | Lactiplantibacillus plantarum | F9USS9 | - |
- |
| 5.1.2.1 | Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1 | F9USS9 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 4.99.1.12 | Strep-Tactin column chromatography | Lactiplantibacillus plantarum |
| 5.1.2.1 | recombinant StrepII-tagged LarA from Lactobacillus lactis by affinity chromatography, gel filtration, and ultrafiltration, to homogeneity. Purification of LarA and LarE can readily be achieved from the strain expressing the entire operon, whereas tagged LarB and LarC can only be purified when the corresponding genes are individually subcloned | Lactiplantibacillus plantarum |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.99.1.12 | Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide | - |
Lactiplantibacillus plantarum | pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni2+ | - |
? | |
| 4.99.1.12 | Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide | - |
Lactiplantibacillus plantarum NCIMB 8826 | pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni2+ | - |
? | |
| 5.1.2.1 | (S)-lactate | - |
Lactiplantibacillus plantarum | (R)-lactate | - |
r | |
| 5.1.2.1 | (S)-lactate | - |
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1 | (R)-lactate | - |
r | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 4.99.1.12 | ? | x * 55000, Strep-tagged enzyme, SDS-PAGE | Lactiplantibacillus plantarum |
| 5.1.2.1 | homodimer | - |
Lactiplantibacillus plantarum |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 4.99.1.12 | LarC | - |
Lactiplantibacillus plantarum |
| 5.1.2.1 | LARa | - |
Lactiplantibacillus plantarum |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 5.1.2.1 | 22 | - |
assay at room temperature | Lactiplantibacillus plantarum |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.2.1 | 1333 | - |
(R)-lactate | pH and temperature not specified in the publication | Lactiplantibacillus plantarum | |
| 5.1.2.1 | 4745 | - |
(S)-lactate | pH and temperature not specified in the publication | Lactiplantibacillus plantarum | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 5.1.2.1 | evolution | analysis of the lar gene cluster and its encoded Lar proteins, phylogenetic tree. 92% of the genomes bearing a larA homologue (102 out of 111 genomes) also contain the genes for the Lar accessory proteins (larBCE), further reinforcing the necessity of these proteins for LarA activation | Lactiplantibacillus plantarum |
| 5.1.2.1 | additional information | LarA catalytic site structure analysis in subunits one and two, overview. Structure comparisons to LarA from Thermus thermophilus | Lactiplantibacillus plantarum |
| 5.1.2.1 | physiological function | lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Four proteins and Ni are required for in vivo Lar activity. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation | Lactiplantibacillus plantarum |
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