pbpD

class A penicillin-binding protein 4

locus: BSU_31490

pI: 9.31

mw: 70.45 kDa

protein length: 624 aa

gene length: 1875 bp

function: bifunctional glucosyltransferase/ transpeptidase

product: penicillin-binding protein 4

essential: no

synonyms

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 1.1.1.7|Penicillin-binding proteins]
• [category|SW 6|Groups of genes] → [category|SW 6.2|Membrane proteins]

Gene

Coordinates: 3,233,911 → 3,235,785

Phenotypes of a mutant

• a strain lacking all four class A [SW|penicillin-binding proteins] ([gene|A8EEC896B279CFDDE9C3A6F146A04EC822E33A4F|ponA] [gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD] [gene|73275060537497E6A9859856C9F040763E36316B|pbpF] [gene|BDC2D775CCE7C06F5619BAC214F29CFC637FE804|pbpG]) is severely inhibited for L-form switching in the presence of D-cycloserine [pubmed|29456081]

The protein

Catalyzed reaction/ biological activity

• highly active transpeptidase, responsible for about 50% of D-amino acid incorporation [pubmed|26499795]
• [GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]_(n)-diphospho-di-trans,octa-cis-undecaprenol + β-D-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphospho-di-trans,octa-cis-undecaprenol --> [GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]_(n+1)-diphospho-di-trans-octa-cis-undecaprenol + di-trans,octa-cis-undecaprenyl diphosphate + H⁺ (according to UniProt)
• Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine (according to UniProt)

Protein family

• N-terminal part: [SW|glycosyltransferase 51 family] (according to UniProt)
• C-terminal part: [SW|transpeptidase family] (according to UniProt)

Paralogous protein(s)

• [protein|73275060537497E6A9859856C9F040763E36316B|PbpF], [protein|BDC2D775CCE7C06F5619BAC214F29CFC637FE804|PbpG], [protein|A8EEC896B279CFDDE9C3A6F146A04EC822E33A4F|PonA]

Structure

• [PDB|3VMA] (PBP1B from ''E. coli'', 28% identity) [Pubmed|19458048]

[SW|Localization]

• cell membrane (according to UniProt)
• during vegetative growth: septal, distinct spots at periphery [pubmed|14731276]

Expression and Regulation

Operons

• genes: [gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD]-[gene|1069B74CDD87706FA00A495AEA04BB89D79EDF21|yuxK]
  description: [Pubmed|7961491]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|7961491], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  additional information

  • the terminator is [protein|search|NusA]-dependent [ http://www.nature.com/articles/nmicrobiol20157 Reference]

Biological materials

Mutant

• BKE31490 (Δ[gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE31490 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACTCTCTTTTCTCCTAAAT, downstream forward: _UP4_TAAAGGATCGGAGGGGATAT
• BKK31490 (Δ[gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK31490 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACTCTCTTTTCTCCTAAAT, downstream forward: _UP4_TAAAGGATCGGAGGGGATAT

GFP fusion

• 2082 [gene|0467447B10EE7C1FDF86022AB6FBDBABFD32A9E5|trpC]2 [gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD]::pSG1490 (cat P_xyl-gfpa-[gene|E50D4B30C2A0987A356C988AF8A4951C0CDF6C06|pbpD]1-510) [pubmed|14731276], available in [SW|Dirk Jan Scheffers]' lab and in the [http://bgsc.org BGSC]

References

• 14731276,8606187,7961491,20487272,28045164,19458048,29456081,26499795