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O53223

- O53223_MYCTO

UniProt

O53223 - O53223_MYCTO

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Protein
Submitted name:

L,d-transpeptidase LdtB

Gene
MT2594, V735_02606
Organism
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Status
Unreviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei204 – 2041Acetate 1
Binding sitei215 – 2151Acetate 2; via amide nitrogen
Metal bindingi232 – 2321Calcium
Metal bindingi234 – 2341Calcium
Metal bindingi235 – 2351Calcium; via amide nitrogen
Metal bindingi236 – 2361Calcium; via amide nitrogen
Binding sitei319 – 3191Acetate 5
Metal bindingi342 – 3421Sodium; via carbonyl oxygenImported
Metal bindingi343 – 3431Sodium; via carbonyl oxygenImported
Metal bindingi345 – 3451Sodium; via carbonyl oxygenImported
Binding sitei352 – 3521Acetate 4
Binding sitei376 – 3761Acetate 3

GO - Molecular functioni

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

GO - Biological processi

  1. peptidoglycan-based cell wall biogenesis Source: MTBBASE
  2. peptidoglycan metabolic process Source: MTBBASE
  3. proteolysis Source: GOC
Complete GO annotation...

Keywords - Ligandi

CalciumImported, Metal-bindingImported, SodiumImported

Enzyme and pathway databases

BioCyciMTBRV:RV2518C-MONOMER.

Names & Taxonomyi

Protein namesi
Submitted name:
L,d-transpeptidase LdtBImported
Submitted name:
Uncharacterized proteinImported
Gene namesi
Ordered Locus Names:MT2594Imported
ORF Names:V735_02606Imported
OrganismiMycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Imported
Taxonomic identifieri83331 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
ProteomesiUP000001020: Chromosome

Organism-specific databases

TubercuListiRv2518c.

Subcellular locationi

GO - Cellular componenti

  1. cell wall Source: MTBBASE
Complete GO annotation...

Interactioni

Protein-protein interaction databases

STRINGi83332.Rv2518c.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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[»]
3VYNX-ray2.50A/B55-408[»]
3VYOX-ray1.80A/B140-408[»]
3VYPX-ray1.40A/B140-408[»]
4GSQX-ray1.80A131-408[»]
4GSRX-ray1.79A131-408[»]
4GSUX-ray2.00A/B131-408[»]
4HU2X-ray1.46A55-250[»]
4HUCX-ray1.86A/B149-408[»]

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni323 – 3242Acetate 6 binding
Regioni385 – 3873Acetate 7 binding

Phylogenomic databases

HOGENOMiHOG000241380.
OMAiNAEWFYD.
OrthoDBiEOG66QKTJ.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

O53223-1 [UniParc]FASTAAdd to Basket

« Hide

MPKVGIAAQA GRTRVRRAWL TALMMTAVMI GAVACGSGRG PAPIKVIADK    50
GTPFADLLVP KLTASVTDGA VGVTVDAPVS VTAADGVLAA VTMVNDNGRP 100
VAGRLSPDGL RWSTTEQLGY NRRYTLNATA LGLGGAATRQ LTFQTSSPAH 150
LTMPYVMPGD GEVVGVGEPV AIRFDENIAD RGAAEKAIKI TTNPPVEGAF 200
YWLNNREVRW RPEHFWKPGT AVDVAVNTYG VDLGEGMFGE DNVQTHFTIG 250
DEVIATADDN TKILTVRVNG EVVKSMPTSM GKDSTPTANG IYIVGSRYKH 300
IIMDSSTYGV PVNSPNGYRT DVDWATQISY SGVFVHSAPW SVGAQGHTNT 350
SHGCLNVSPS NAQWFYDHVK RGDIVEVVNT VGGTLPGIDG LGDWNIPWDQ 400
WRAGNAKA 408
Length:408
Mass (Da):43,366
Last modified:June 1, 1998 - v1
Checksum:i8705AA9136A0D495
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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:
PDBe
RCSB PDB
PDBj
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 [» ]
3VYN X-ray 2.50 A/B 55-408 [» ]
3VYO X-ray 1.80 A/B 140-408 [» ]
3VYP X-ray 1.40 A/B 140-408 [» ]
4GSQ X-ray 1.80 A 131-408 [» ]
4GSR X-ray 1.79 A 131-408 [» ]
4GSU X-ray 2.00 A/B 131-408 [» ]
4HU2 X-ray 1.46 A 55-250 [» ]
4HUC X-ray 1.86 A/B 149-408 [» ]
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.

Organism-specific databases

TubercuListi Rv2518c.

Phylogenomic databases

HOGENOMi HOG000241380.
OMAi NAEWFYD.
OrthoDBi EOG66QKTJ.

Enzyme and pathway databases

BioCyci MTBRV:RV2518C-MONOMER.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CDC 1551 / Oshkosh and CDC1551Imported.
  2. Cited for: NUCLEOTIDE SEQUENCE.
    Strain: CDC1551.
  3. "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.
  4. "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.
  5. "Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains."
    Kim H.S., Kim J., Im H.N., Yoon J.Y., An D.R., Yoon H.J., Kim J.Y., Min H.K., Kim S.J., Lee J.Y., Han B.W., Suh S.W.
    Acta Crystallogr. D 69:420-431(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) OF 131-408 IN COMPLEX WITH CALCIUM.
  6. "Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis."
    Both D., Steiner E.M., Stadler D., Lindqvist Y., Schnell R., Schneider G.
    Acta Crystallogr. D 69:432-441(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS) OF 55-250 IN COMPLEX WITH SODIUM.
  7. "Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis."
    Li W.J., Li D.F., Hu Y.L., Zhang X.E., Bi L.J., Wang D.C.
    Cell Res. 23:728-731(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF 140-408.
  8. Cited for: NUCLEOTIDE SEQUENCE.
    Strain: Cdc1551Imported.

Entry informationi

Entry nameiO53223_MYCTO
AccessioniPrimary (citable) accession number: O53223
Secondary accession number(s): F2GH40, Q7D6Z8
Entry historyi
Integrated into UniProtKB/TrEMBL: June 1, 1998
Last sequence update: June 1, 1998
Last modified: September 3, 2014
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Complete proteome

External Data

Dasty 3

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