alr

alanine racemase

locus: BSU_04640

pI: 8.43

mw: 43.10 kDa

protein length: 389 aa

gene length: 1167 bp

function: peptidoglycan biosynthesis

product: alanine racemase

essential: yes

ec: 5.1.1.1

synonyms: dal,alrA

Genomic Context

categories

• [category|SW 1|Cellular processes] → [category|SW 1.1|Cell envelope and cell division] → [category|SW 1.1.1|Cell wall synthesis] → [category|SW 1.1.1.1|Biosynthesis of peptidoglycan]
• [category|SW 2|Metabolism] → [category|SW 2.3|Amino acid/ nitrogen metabolism] → [category|SW 2.3.1|Biosynthesis/ acquisition of amino acids] → [category|SW 2.3.1.15|Biosynthesis/acquisition of L- and D-alanine]
• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.1|Biosynthesis of cell wall components] → [category|SW 2.6.1.1|Biosynthesis of peptidoglycan]
• [category|SW 6|Groups of genes] → [category|SW 6.1|Essential genes]

Gene

Coordinates: 517,372 → 518,541

Phenotypes of a mutant

• reported to be essential [Pubmed|12682299], however deletion mutants have been reported by Ferrari et al. (1985) and Xia et al (2007) [Pubmed|17602222]
• auxotrophy for D-alanine
• a [gene|219586A3F378DC38EA076FD39B99D41136BDE722|ytnA] [gene|CB0B6C69CB5CFF6FE30C3F95991F309C8DE1E344|alr] double mutant is not viable due to the inability to acquire D-alanine [https://www.biorxiv.org/content/10.1101/562850v2 reference]

The protein

Catalyzed reaction/ biological activity

• L-alanine --> D-alanine (according to UniProt)

Protein family

• alanine racemase family (with [protein|E267F2B6448E380B354AE091734E4AC4DB5825EF|YncD], according to UniProt)

Paralogous protein(s)

• [protein|E267F2B6448E380B354AE091734E4AC4DB5825EF|YncD]

[SW|Cofactors]

• PLP (according to UniProt)

Structure

• [PDB|1L6G] (with N-[5�-phosphopyridoxyl]-D-alanine, Geobacillus stearothermophilus), [PDB|1SFT] (Geobacillus stearothermophilus)

Expression and Regulation

Operons

• genes: [gene|CB0B6C69CB5CFF6FE30C3F95991F309C8DE1E344|alr]-[gene|052BD59112DBE2F1DAC9DA5A7B0EA8DAF8D6FC47|ndoAI]-[gene|2E5A557E417CB355331CC0555D46A79793EB90B3|ndoA]
  description: [pubmed|22383849]

Biological materials

Mutant

• [http://www.ncbi.nlm.nih.gov/nuccore/402479429?report=genbank&from=517383&to=518551 alr-1], two-base mutation 526AG>T (=R176X), creating a frameshift and an immediate stop codon, available in [http://www.bgsc.org/ BGSC] 1A4, a D-alanine auxotroph

References

• Ferrari E, Henner DJ, Yang MY. Isolation of an Alanine Racemase Gene from Bacillus subtilis and its Use for Plasmid Maintenance in B. subtilis, Nature Biotechnol 1985.Nov;3:1003-7.
• 3138014
• 17602222