LDT5_MYCTO
ID LDT5_MYCTO Reviewed; 451 AA.
AC P9WKV2; L0T6T6; P64703; Q11149;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=L,D-transpeptidase 5;
DE Short=LDT 5;
DE EC=2.3.2.-;
DE AltName: Full=Ldt(Mt5);
GN OrderedLocusNames=MT0501;
OS Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83331;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CDC 1551 / Oshkosh;
RX PubMed=12218036; DOI=10.1128/jb.184.19.5479-5490.2002;
RA Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O.,
RA Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K.,
RA Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L.,
RA Delcher A., Utterback T.R., Weidman J.F., Khouri H.M., Gill J., Mikula A.,
RA Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.;
RT "Whole-genome comparison of Mycobacterium tuberculosis clinical and
RT laboratory strains.";
RL J. Bacteriol. 184:5479-5490(2002).
RN [2]
RP DISRUPTION PHENOTYPE.
RC STRAIN=CDC 1551 / Oshkosh;
RX PubMed=20305661; DOI=10.1038/nm.2120;
RA Gupta R., Lavollay M., Mainardi J.L., Arthur M., Bishai W.R.,
RA Lamichhane G.;
RT "The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical
RT transpeptidase required for virulence and resistance to amoxicillin.";
RL Nat. Med. 16:466-469(2010).
CC -!- FUNCTION: Generates 3->3 cross-links in peptidoglycan, catalyzing the
CC cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and
CC the formation of a bond between the carbonyl of mDap(3) of the donor
CC stem and the side chain of mDap(3) of the acceptor stem. Is specific
CC for donor substrates containing a stem tetrapeptide since it cannot use
CC pentapeptide stems (By similarity). {ECO:0000250}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene have morphologies and
CC growth phenotypes similar to those of the wild-type strain.
CC {ECO:0000269|PubMed:20305661}.
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DR EMBL; AE000516; AAK44724.1; -; Genomic_DNA.
DR PIR; F70743; F70743.
DR RefSeq; WP_003402357.1; NZ_KK341227.1.
DR PDB; 4ZFQ; X-ray; 2.80 A; A=1-451.
DR PDBsum; 4ZFQ; -.
DR AlphaFoldDB; P9WKV2; -.
DR SMR; P9WKV2; -.
DR EnsemblBacteria; AAK44724; AAK44724; MT0501.
DR KEGG; mtc:MT0501; -.
DR PATRIC; fig|83331.31.peg.531; -.
DR HOGENOM; CLU_039404_3_0_11; -.
DR BRENDA; 2.3.2.12; 3445.
DR BRENDA; 2.3.2.B14; 3445.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001020; Chromosome.
DR GO; GO:0016746; F:acyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR CDD; cd16913; YkuD_like; 1.
DR Gene3D; 2.40.440.10; -; 1.
DR InterPro; IPR041280; Big_10.
DR InterPro; IPR005490; LD_TPept_cat_dom.
DR InterPro; IPR038063; Transpep_catalytic_dom.
DR Pfam; PF17964; Big_10; 1.
DR Pfam; PF03734; YkuD; 1.
DR SUPFAM; SSF141523; SSF141523; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Cell shape;
KW Cell wall biogenesis/degradation; Peptidoglycan synthesis; Transferase.
FT CHAIN 1..451
FT /note="L,D-transpeptidase 5"
FT /id="PRO_0000103685"
FT DOMAIN 264..383
FT /note="YkuD"
FT REGION 417..451
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 342
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 360
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 323
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 337..338
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 362
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 85..100
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 128..136
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 162..164
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 187..191
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 194..200
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 217..224
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 253..259
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 273..278
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 281..287
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 302..306
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 310..314
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 340..343
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 365..374
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 380..385
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 387..389
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 392..394
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 399..401
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT HELIX 404..409
FT /evidence="ECO:0007829|PDB:4ZFQ"
FT STRAND 411..413
FT /evidence="ECO:0007829|PDB:4ZFQ"
SQ SEQUENCE 451 AA; 47891 MW; 72660F467FFA0A38 CRC64;
MVIRVLFRPV SLIPVNNSST PQSQGPISRR LALTALGFGV LAPNVLVACA GKVTKLAEKR
PPPAPRLTFR PADSAADVVP IAPISVEVGD GWFQRVALTN SAGKVVAGAY SRDRTIYTIT
EPLGYDTTYT WSGSAVGHDG KAVPVAGKFT TVAPVKTINA GFQLADGQTV GIAAPVIIQF
DSPISDKAAV ERALTVTTDP PVEGGWAWLP DEAQGARVHW RPREYYPAGT TVDVDAKLYG
LPFGDGAYGA QDMSLHFQIG RRQVVKAEVS SHRIQVVTDA GVIMDFPCSY GEADLARNVT
RNGIHVVTEK YSDFYMSNPA AGYSHIHERW AVRISNNGEF IHANPMSAGA QGNSNVTNGC
INLSTENAEQ YYRSAVYGDP VEVTGSSIQL SYADGDIWDW AVDWDTWVSM SALPPPAAKP
AATQIPVTAP VTPSDAPTPS GTPTTTNGPG G
