Rv2518c (ldtB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: lipoprotein lppS
- REFSEQ: lipoprotein LppS
- PATRIC: Lipoprotein LppS
- TUBERCULIST: Probable LD-transpeptidase LdtB
- NCBI: Probable L,D-transpeptidase LdtB
- updated information (H37Rv4):
  - gene name: ldtB
  - function: (3,3-) L,D-transpeptidase, peptidoglycan synthesis
  - reference: Cordillot (2013) PMC3837840
Type: Essential
Start: 2834109
End: 2835335
Operon:

Trans-membrane region:
Role: II.C.1 - Lipoproteins(lppA-lpr0)
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0016746 - transferase activity, transferring acyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
- GO:0008360 - regulation of cell shape (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0071972 - peptidoglycan L,D-transpeptidase activity (FLUTE) (FLUTE Assigned!)
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: 4huc, 3vyo, 3vyn, 4gsq, 4gsr, 4hu2, 4gsu, 3tx4, 3u1p, 3u1q, 3vyp, 3vae, 3tur
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
6RRM	100%	Mycobacterium tuberculosis CDC1551	Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen
6RLG	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of LdtMt2 from Mycobacterium tuberculosis
6IYW	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with Imipenem adduct
6IYV	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ertapenem adduct
6BOI	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354
5K69	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224
5E1I	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210
5E1G	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208
5DZP	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation B
5DZJ	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation A

Links to additional information on ldtB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -2.936 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MPKVGIAAQAGRTRVRRAWLTALMMTAVMIGAVACGSGRGPAPIKVIADKGTPFADLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRP
VAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAF
YWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKH
IIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQ
WRAGNAKA

(Nucleotide sequence available on KEGG)

Additional Information

MT2594/LdtMt2/LdtB, (3,3-) L,D-transpeptidase, peptidoglycan synthesis
Gupta et al (2010). Nat Med. http://www.ncbi.nlm.nih.gov/pubmed/20305661
essential for virulence in mice

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 20 non-insertions in a row out of 21 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.965700; 8 non-insertions in a row out of 21 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.998700; 11 non-insertions in a row out of 21 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.976550; 9 non-insertions in a row out of 22 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.897200; 8 non-insertions in a row out of 22 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0273c (-) (Direct binding)
- Rv1473A (-) (Direct binding)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0465c (-)

Property	Value	Creator	Evidence	Comment
Interaction	RegulatedBy Rv2711	yamir.moreno	TAS	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Symbol	ldtB	mjackson	IMP	Peptidoglycan assembly/maturation
Name	L,D-transpeptidase	mjackson	IMP	Peptidoglycan assembly/maturation
Symbol	ldtB	mjackson	IDA	Peptidoglycan assembly/maturation
Name	L,D-transpeptidase	mjackson	IDA	Peptidoglycan assembly/maturation

TB Genome Annotation Portal