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ddl

D-alanine-D-alanine ligase

locus: BSU_04560

pI: 4.58

mw: 38.97 kDa

protein length: 354 aa

gene length: 1065 bp

function: peptidoglycan precursor biosynthesis

product: D-alanine-D-alanine ligase

essential: yes

ec: 6.3.2.4

synonyms: ddlA

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 2.6|Additional metabolic pathways] → [category|SW 2.6.1|Biosynthesis of cell wall components] → [category|SW 2.6.1.1|Biosynthesis of peptidoglycan]
• [category|SW 4|Lifestyles] → [category|SW 4.3|Coping with stress] → [category|SW 4.3.2|Cell envelope stress proteins (controlled by SigM, V, W, X, Y)]
• [category|SW 6|Groups of genes] → [category|SW 6.1|Essential genes]

Gene

Coordinates: 508,248 509,312

Phenotypes of a mutant

• essential [Pubmed|12682299]

The protein

Catalyzed reaction/ biological activity

• ATP + 2 D-alanine --> ADP + phosphate + D-alanyl-D-alanine (according to UniProt)

Protein family

• D-alanine--D-alanine ligase family (single member, according to UniProt)

[SW|Domains]

• [SW|ATP-grasp doamin] (aa 133-338) (according to UniProt)

Structure

• [PDB|2YZG] (from ''Thermus thermophilus hb8 mutant'', 40% identity, 53% similarity)

[SW|Localization]

• cytoplasm (according to Swiss-Prot)

Expression and Regulation

Operons

• genes: [gene|A47DBF8546E0F726A0FE58C21D3F28150290DF7F|ddl]-[gene|EC9F1D4F1863E53A818A51B0E16B201A251F077E|murF]
  description: [Pubmed|22383849]

  sigma factors

  • [protein|081DF3EE9FA56209D648C7677188C61CE3AA8E41|SigM]: sigma factor, [Pubmed|18179421], in [regulon|081DF3EE9FA56209D648C7677188C61CE3AA8E41|SigM regulon]
  • [protein|D04629D798E458AD538809BB2B150B7FA81D2C7E|SigV]: sigma factor, in [regulon|D04629D798E458AD538809BB2B150B7FA81D2C7E|SigV regulon]

  regulation

  • expression is reduced in a [protein|D04629D798E458AD538809BB2B150B7FA81D2C7E|SigV] mutant [Pubmed|21926231]
  • the leader mRNA is processed upstream of [gene|A47DBF8546E0F726A0FE58C21D3F28150290DF7F|ddl] by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y], this requires the [protein|EE52DFA35B935E551871D079A9BE877DB2001A3B|YmcA]-[protein|6C9A092F38739A3759793EF8B496569CD02C2E3F|YlbF]-[protein|EBD15C174A03B7FCDFFE4C5DB5D86E93F1B9CAC4|YaaT] complex [Pubmed|29794222]

Biological materials

Mutant

• MGNA-C104 (ddlA::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/2102 NBRP B. subtilis, Japan]

References

• 18179421,29794222