TB Genome Annotation Portal

Rv0116c (ldtA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: hypothetical protein
  • REFSEQ: hypothetical protein
  • PATRIC: Possible membrane protein
  • TUBERCULIST: Probable LD-transpeptidase LdtA
  • NCBI: Probable L,D-transpeptidase LdtA
  • updated information (H37Rv4):
    • gene name: ldtA
    • function: (3,3-) L,D-transpeptidase, peptidoglycan synthesis
    • reference: Cordillot (2013) PMC3837840
• Type: Not Target
• Start: 140267
• End: 141022
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0071972 - peptidoglycan L,D-transpeptidase activity (Uniprot)
  • GO:0071555 - cell wall organization (Uniprot)
  • GO:0042597 - periplasmic space (Uniprot)
  • GO:0018104 - peptidoglycan-protein cross-linking (Uniprot)
  • GO:0016746 - transferase activity, transferring acyl groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
  • GO:0008360 - regulation of cell shape (Uniprot)
  • GO:0006508 - proteolysis (Uniprot)
  • GO:0005576 - extracellular region (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  5E5L	100%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 Angstrom
  5E51	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 with Faropenem adduct
  4JMX	100%	Mycobacterium tuberculosis	Structure of LD transpeptidase LdtMt1 in complex with imipenem
  4JMN	100%	Mycobacterium tuberculosis	Crystal structure of LD transpeptidase LdtMt1 from M. tuberculosis
  4XVO	64%	Mycobacterium smegmatis	L,D-transpeptidase from Mycobacterium smegmatis
  6D51	50%	Mycobacterium tuberculosis	Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis in complex with a faropenem-derived adduct
  6D4K	50%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution
  4K73	50%	Mycobacterium tuberculosis	X-ray crystal structure of an L,D-transpeptidase from Mycobacterium tuberculosis H37Rv
  6RRM	43%	Mycobacterium tuberculosis CDC1551	Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen
  6RLG	43%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of LdtMt2 from Mycobacterium tuberculosis

• Links to additional information on ldtA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.774 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MRRVVRYLSVVVAITLMLTAESVSIATAAVPPLQPIPGVASVSPANGAVVGVAHPVVVTFTTPVTDRRAVERSIRISTPHNTTGHFEWVASNVVRWVPHR
YWPPHTRVSVGVQELTEGFETGDALIGVASISAHTFTVSRNGEVLRTMPASLGKPSRPTPIGSFHAMSKERTVVMDSRTIGIPLNSSDGYLLTAHYAVRV
TWSGVYVHSAPWSVNSQGYANVSHGCINLSPDNAAWYFDAVTVGDPIEVVG

Additional Information

LdtMt1/LdtA, (3,3-) L,D-transpeptidase, peptidoglycan synthesis
http://jb.asm.org/content/190/12/4360
Dubee et al (2012). AAC. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421625/