ID   LDT5_MYCBO              Reviewed;         451 AA.
AC   P64704; A0A1R3XVI0; Q11149; X2BF28;
DT   11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2004, sequence version 1.
DT   03-AUG-2022, entry version 90.
DE   RecName: Full=L,D-transpeptidase Mb0493;
DE            Short=LDT Mb0493;
DE            EC=2.3.2.-;
GN   OrderedLocusNames=BQ2027_MB0493;
OS   Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=233413;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-935 / AF2122/97;
RX   PubMed=12788972; DOI=10.1073/pnas.1130426100;
RA   Garnier T., Eiglmeier K., Camus J.-C., Medina N., Mansoor H., Pryor M.,
RA   Duthoy S., Grondin S., Lacroix C., Monsempe C., Simon S., Harris B.,
RA   Atkin R., Doggett J., Mayes R., Keating L., Wheeler P.R., Parkhill J.,
RA   Barrell B.G., Cole S.T., Gordon S.V., Hewinson R.G.;
RT   "The complete genome sequence of Mycobacterium bovis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:7877-7882(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC   STRAIN=ATCC BAA-935 / AF2122/97;
RX   PubMed=28385856; DOI=10.1128/genomea.00157-17;
RA   Malone K.M., Farrell D., Stuber T.P., Schubert O.T., Aebersold R.,
RA   Robbe-Austerman S., Gordon S.V.;
RT   "Updated reference genome sequence and annotation of Mycobacterium bovis
RT   AF2122/97.";
RL   Genome Announc. 5:E00157-E00157(2017).
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.
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DR   EMBL; LT708304; SIT99088.1; -; Genomic_DNA.
DR   RefSeq; NP_854156.1; NC_002945.3.
DR   RefSeq; WP_003402357.1; NC_002945.4.
DR   AlphaFoldDB; P64704; -.
DR   SMR; P64704; -.
DR   PATRIC; fig|233413.5.peg.535; -.
DR   OMA; PSHRMQV; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000001419; 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   3: Inferred from homology;
KW   Acyltransferase; Cell shape; Cell wall biogenesis/degradation;
KW   Peptidoglycan synthesis; Transferase.
FT   CHAIN           1..451
FT                   /note="L,D-transpeptidase Mb0493"
FT                   /id="PRO_0000103686"
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"
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