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Protein

L,D-transpeptidase 2

Gene

ldtB

Organism
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala4 bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap3 of the donor stem and the side chain of mDap3 of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems. Is essential for virulence in a mouse model of acute infection.1 Publication

Enzyme regulationi

Is irreversibly inactivated by the beta-lactams carbapenems via the formation of a covalent adduct resulting from acylation of the catalytic Cys.By similarity

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi232CalciumBy similarity1
Metal bindingi235Calcium; via amide nitrogenBy similarity1
Metal bindingi236Calcium; via amide nitrogenBy similarity1
Binding sitei318Substrate1
Active sitei336Proton donor/acceptor1 Publication1
Active sitei354Nucleophile1 Publication1
Sitei354Binds to carbapenem drug (covalent)By similarity1
Binding sitei356Substrate1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Virulence

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciMTBCDC1551:GT3Z-7043-MONOMER.
BRENDAi2.3.2.12. 3445.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
L,D-transpeptidase 2 (EC:2.3.2.-)
Short name:
LDT 2
Alternative name(s):
Ldt(Mt2)
Gene namesi
Name:ldtB
Ordered Locus Names:MT2594
ORF Names:V735_02606
OrganismiMycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Taxonomic identifieri83331 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001020 Componenti: Chromosome

Subcellular locationi

  • Cell membrane PROSITE-ProRule annotation; Lipid-anchor PROSITE-ProRule annotation

GO - Cellular componenti

  • cell wall Source: MTBBASE
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Inactivation of this gene leads to altered colony morphology and growth, attenuation of persistence and increased susceptibility to amoxicillin-clavulanate both in vitro and in the mouse model during the chronic phase of infection. Loss of both ldtMt1 and ldtMt2 results in phenotypes that are unique and/or severe compared to the single mutants lacking only ldtMt1 or ldtMt2. The double gene deletion severely alters cellular shape, intracellular morphology, physiology and virulence: the length of mutant cells are shorter than wild-type, they have deep surface depressions and bulges, they possess large unstained vacuole-like structures, the thickness of the peptidoglycan layer is smaller, the protein localization is altered, and in vitro and in vivo growth and virulence are severly attenuated. Moreover, double-mutant cells are more sensitive to vancomycin and amoxicillin-clavulanate.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 34PROSITE-ProRule annotationAdd BLAST34
ChainiPRO_000043033335 – 408L,D-transpeptidase 2Add BLAST374

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi35N-palmitoyl cysteinePROSITE-ProRule annotation1
Lipidationi35S-diacylglycerol cysteinePROSITE-ProRule annotation1

Keywords - PTMi

Lipoprotein, Palmitate

Expressioni

Inductioni

Is expressed at a level higher than other LDT paralogs at all phases of growth.1 Publication

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1408
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi125 – 127Combined sources3
Beta strandi154 – 158Combined sources5
Beta strandi170 – 176Combined sources7
Helixi181 – 187Combined sources7
Beta strandi188 – 194Combined sources7
Beta strandi198 – 204Combined sources7
Beta strandi207 – 214Combined sources8
Beta strandi221 – 227Combined sources7
Beta strandi238 – 240Combined sources3
Beta strandi242 – 249Combined sources8
Beta strandi253 – 258Combined sources6
Turni259 – 261Combined sources3
Beta strandi263 – 268Combined sources6
Beta strandi271 – 277Combined sources7
Beta strandi289 – 293Combined sources5
Beta strandi297 – 304Combined sources8
Helixi305 – 308Combined sources4
Beta strandi319 – 327Combined sources9
Beta strandi334 – 337Combined sources4
Helixi339 – 341Combined sources3
Turni342 – 347Combined sources6
Beta strandi351 – 357Combined sources7
Helixi359 – 368Combined sources10
Beta strandi374 – 379Combined sources6
Beta strandi389 – 391Combined sources3
Helixi393 – 395Combined sources3
Helixi398 – 403Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TURX-ray1.72A/B122-408[»]
3TX4X-ray2.32A/B122-408[»]
3U1PX-ray2.80A/B122-408[»]
3U1QX-ray2.40A/B122-408[»]
3VAEX-ray2.80A/B122-408[»]
ProteinModelPortaliO53223.
SMRiO53223.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini259 – 377YkuDAdd BLAST119

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni331 – 332Substrate binding2

Sequence similaritiesi

Contains 1 YkuD domain.Curated

Keywords - Domaini

Signal

Phylogenomic databases

HOGENOMiHOG000241380.
InParanoidiO53223.
OrthoDBiPOG091H08EZ.

Family and domain databases

InterProiIPR005490. LD_TPept_cat_dom.
[Graphical view]
PfamiPF03734. YkuD. 1 hit.
[Graphical view]
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O53223-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKVGIAAQA GRTRVRRAWL TALMMTAVMI GAVACGSGRG PAPIKVIADK
60 70 80 90 100
GTPFADLLVP KLTASVTDGA VGVTVDAPVS VTAADGVLAA VTMVNDNGRP
110 120 130 140 150
VAGRLSPDGL RWSTTEQLGY NRRYTLNATA LGLGGAATRQ LTFQTSSPAH
160 170 180 190 200
LTMPYVMPGD GEVVGVGEPV AIRFDENIAD RGAAEKAIKI TTNPPVEGAF
210 220 230 240 250
YWLNNREVRW RPEHFWKPGT AVDVAVNTYG VDLGEGMFGE DNVQTHFTIG
260 270 280 290 300
DEVIATADDN TKILTVRVNG EVVKSMPTSM GKDSTPTANG IYIVGSRYKH
310 320 330 340 350
IIMDSSTYGV PVNSPNGYRT DVDWATQISY SGVFVHSAPW SVGAQGHTNT
360 370 380 390 400
SHGCLNVSPS NAQWFYDHVK RGDIVEVVNT VGGTLPGIDG LGDWNIPWDQ

WRAGNAKA
Length:408
Mass (Da):43,366
Last modified:June 1, 1998 - v1
Checksum:i8705AA9136A0D495
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000516 Genomic DNA. Translation: AAK46901.1.
JLBH01000002 Genomic DNA. Translation: KBN13754.1.
PIRiC70870.
RefSeqiWP_003412938.1. NZ_KK341227.1.

Genome annotation databases

EnsemblBacteriaiAAK46901; AAK46901; MT2594.
KBN13754; KBN13754; V735_02606.
KEGGimtc:MT2594.
PATRICi18127458. VBIMycTub22151_2833.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000516 Genomic DNA. Translation: AAK46901.1.
JLBH01000002 Genomic DNA. Translation: KBN13754.1.
PIRiC70870.
RefSeqiWP_003412938.1. NZ_KK341227.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TURX-ray1.72A/B122-408[»]
3TX4X-ray2.32A/B122-408[»]
3U1PX-ray2.80A/B122-408[»]
3U1QX-ray2.40A/B122-408[»]
3VAEX-ray2.80A/B122-408[»]
ProteinModelPortaliO53223.
SMRiO53223.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK46901; AAK46901; MT2594.
KBN13754; KBN13754; V735_02606.
KEGGimtc:MT2594.
PATRICi18127458. VBIMycTub22151_2833.

Phylogenomic databases

HOGENOMiHOG000241380.
InParanoidiO53223.
OrthoDBiPOG091H08EZ.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciMTBCDC1551:GT3Z-7043-MONOMER.
BRENDAi2.3.2.12. 3445.

Family and domain databases

InterProiIPR005490. LD_TPept_cat_dom.
[Graphical view]
PfamiPF03734. YkuD. 1 hit.
[Graphical view]
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLDT2_MYCTO
AccessioniPrimary (citable) accession number: O53223
Secondary accession number(s): F2GH40, Q7D6Z8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 2014
Last sequence update: June 1, 1998
Last modified: November 2, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.