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O53223

- LDT2_MYCTO

UniProt

O53223 - LDT2_MYCTO

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Protein

L,D-transpeptidase 2

Gene

ldtB

Organism
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Status
Reviewed - 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi232 – 2321CalciumBy similarity
Metal bindingi235 – 2351Calcium; via amide nitrogenBy similarity
Metal bindingi236 – 2361Calcium; via amide nitrogenBy similarity
Binding sitei318 – 3181Substrate
Active sitei336 – 3361Proton donor/acceptor1 Publication
Active sitei354 – 3541Nucleophile1 Publication
Sitei354 – 3541Binds to carbapenem drug (covalent)By similarity
Binding sitei356 – 3561Substrate

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. peptidoglycan L,D-transpeptidase activity Source: MTBBASE
  3. transferase activity, transferring acyl groups Source: UniProtKB-KW

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. pathogenesis Source: UniProtKB-KW
  3. peptidoglycan-based cell wall biogenesis Source: MTBBASE
  4. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  5. peptidoglycan metabolic process Source: MTBBASE
  6. proteolysis Source: GOC
  7. regulation of cell shape Source: UniProtKB-KW
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

BioCyciMTBRV:RV2518C-MONOMER.
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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
ProteomesiUP000001020: Chromosome

Subcellular locationi

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

GO - Cellular componenti

  1. cell wall Source: MTBBASE
  2. plasma membrane Source: UniProtKB-KW
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)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3434PROSITE-ProRule annotationAdd
BLAST
Chaini35 – 408374L,D-transpeptidase 2PRO_0000430333Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi35 – 351N-palmitoyl cysteinePROSITE-ProRule annotation
Lipidationi35 – 351S-diacylglycerol cysteinePROSITE-ProRule annotation

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

Protein-protein interaction databases

STRINGi83332.Rv2518c.

Structurei

Secondary structure

1
408
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi125 – 1273Combined sources
Beta strandi154 – 1585Combined sources
Beta strandi170 – 1767Combined sources
Helixi181 – 1877Combined sources
Beta strandi188 – 1947Combined sources
Beta strandi198 – 2047Combined sources
Beta strandi207 – 2148Combined sources
Beta strandi221 – 2277Combined sources
Beta strandi238 – 2403Combined sources
Beta strandi242 – 2498Combined sources
Beta strandi253 – 2586Combined sources
Turni259 – 2613Combined sources
Beta strandi263 – 2686Combined sources
Beta strandi271 – 2777Combined sources
Beta strandi289 – 2935Combined sources
Beta strandi297 – 3048Combined sources
Helixi305 – 3084Combined sources
Beta strandi319 – 3279Combined sources
Beta strandi334 – 3374Combined sources
Helixi339 – 3413Combined sources
Turni342 – 3476Combined sources
Beta strandi351 – 3577Combined sources
Helixi359 – 36810Combined sources
Beta strandi374 – 3796Combined sources
Beta strandi389 – 3913Combined sources
Helixi393 – 3953Combined sources
Helixi398 – 4036Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 58-406.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini259 – 377119YkuDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni331 – 3322Substrate binding

Sequence similaritiesi

Contains 1 YkuD domain.Curated

Keywords - Domaini

Signal

Phylogenomic databases

HOGENOMiHOG000241380.
InParanoidiO53223.
OMAiNAEWFYD.
OrthoDBiEOG66QKTJ.

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.
RefSeqiNP_337087.1. NC_002755.2.

Genome annotation databases

EnsemblBacteriaiAAK46901; AAK46901; MT2594.
CCP45312; CCP45312; Rv2518c.
GeneIDi925826.
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 .
PIRi C70870.
RefSeqi NP_337087.1. NC_002755.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3TUR X-ray 1.72 A/B 122-408 [» ]
3TX4 X-ray 2.32 A/B 122-408 [» ]
3U1P X-ray 2.80 A/B 122-408 [» ]
3U1Q X-ray 2.40 A/B 122-408 [» ]
3VAE X-ray 2.80 A/B 122-408 [» ]
ProteinModelPortali O53223.
SMRi O53223. Positions 58-406.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 83332.Rv2518c.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAK46901 ; AAK46901 ; MT2594 .
CCP45312 ; CCP45312 ; Rv2518c .
GeneIDi 925826.
KEGGi mtc:MT2594.
PATRICi 18127458. VBIMycTub22151_2833.

Phylogenomic databases

HOGENOMi HOG000241380.
InParanoidi O53223.
OMAi NAEWFYD.
OrthoDBi EOG66QKTJ.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci MTBRV:RV2518C-MONOMER.

Family and domain databases

InterProi IPR005490. LD_TPept_cat_dom.
[Graphical view ]
Pfami PF03734. YkuD. 1 hit.
[Graphical view ]
PROSITEi PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CDC 1551 / Oshkosh.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CDC 1551 / Oshkosh.
  3. "The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin."
    Gupta R., Lavollay M., Mainardi J.L., Arthur M., Bishai W.R., Lamichhane G.
    Nat. Med. 16:466-469(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE, INDUCTION.
    Strain: CDC 1551 / Oshkosh.
  4. "Nonclassical transpeptidases of Mycobacterium tuberculosis alter cell size, morphology, the cytosolic matrix, protein localization, virulence, and resistance to beta-lactams."
    Schoonmaker M.K., Bishai W.R., Lamichhane G.
    J. Bacteriol. 196:1394-1402(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: CDC 1551 / Oshkosh.
  5. "The structure of Mycobacterium tuberculosis L,D-transpeptidase 2 provides insights into targeting the cell wall of persisters."
    Erdemli S.B., Gupta R., Lamichhane G., Bishai W., Amzel L.M., Bianchet M.A.
    Submitted (SEP-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 122-408.
    Strain: CDC 1551 / Oshkosh.
  6. "Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2."
    Erdemli S.B., Gupta R., Bishai W.R., Lamichhane G., Amzel L.M., Bianchet M.A.
    Structure 20:2103-2115(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS) OF 122-408 OF WILD-TYPE AND MUTANT ALA-354 IN COMPLEX WITH A PEPTIDOGLYCAN FRAGMENT, REACTION MECHANISM, ACTIVE SITE, SUBUNIT.
    Strain: CDC 1551 / Oshkosh.

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 26, 2014
This is version 86 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

External Data

Dasty 3