LDT5_MYCTU
ID LDT5_MYCTU Reviewed; 451 AA.
AC P9WKV3; 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 36.
DE RecName: Full=L,D-transpeptidase 5;
DE Short=LDT 5;
DE EC=2.3.2.-;
DE AltName: Full=Ldt(Mt5);
GN Name=lprQ; OrderedLocusNames=Rv0483; ORFNames=MTCY20G9.09;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND ACTIVITY
RP REGULATION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=24041897; DOI=10.1128/aac.01663-13;
RA Cordillot M., Dubee V., Triboulet S., Dubost L., Marie A., Hugonnet J.E.,
RA Arthur M., Mainardi J.L.;
RT "In vitro cross-linking of Mycobacterium tuberculosis peptidoglycan by L,D-
RT transpeptidases and inactivation of these enzymes by carbapenems.";
RL Antimicrob. Agents Chemother. 57:5940-5945(2013).
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. {ECO:0000269|PubMed:24041897}.
CC -!- ACTIVITY REGULATION: In contrast to other LDT paralogs, LdtMt5 is not
CC inactivated by the beta-lactams carbapenems, which don't form a
CC covalent adduct with the enzyme. {ECO:0000269|PubMed:24041897}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
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DR EMBL; AL123456; CCP43217.1; -; Genomic_DNA.
DR PIR; F70743; F70743.
DR RefSeq; NP_214997.1; NC_000962.3.
DR RefSeq; WP_003402357.1; NZ_NVQJ01000002.1.
DR PDB; 1U8R; X-ray; 2.75 A; A/B/C/D/G/H/I/J=1-230.
DR PDB; 2ISZ; X-ray; 2.40 A; A/B/C/D=1-140.
DR PDB; 2IT0; X-ray; 2.60 A; A/B/C/D=1-140.
DR PDB; 6D5A; X-ray; 2.62 A; A=50-416.
DR PDBsum; 1U8R; -.
DR PDBsum; 2ISZ; -.
DR PDBsum; 2IT0; -.
DR PDBsum; 6D5A; -.
DR AlphaFoldDB; P9WKV3; -.
DR SMR; P9WKV3; -.
DR STRING; 83332.Rv0483; -.
DR PaxDb; P9WKV3; -.
DR DNASU; 887167; -.
DR GeneID; 887167; -.
DR KEGG; mtu:Rv0483; -.
DR PATRIC; fig|83332.111.peg.530; -.
DR TubercuList; Rv0483; -.
DR eggNOG; COG1376; Bacteria.
DR OMA; PSHRMQV; -.
DR PhylomeDB; P9WKV3; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005576; C:extracellular region; HDA:MTBBASE.
DR GO; GO:0016746; F:acyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0018104; P:peptidoglycan-protein cross-linking; IBA:GO_Central.
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;
KW Reference proteome; Transferase.
FT CHAIN 1..451
FT /note="L,D-transpeptidase 5"
FT /id="PRO_0000430359"
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:6D5A"
FT STRAND 85..99
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:6D5A"
FT TURN 112..115
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 128..136
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 155..158
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 176..182
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 187..191
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 194..200
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 217..224
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 253..259
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 264..268
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 273..278
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 281..287
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 302..306
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 310..313
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 329..335
FT /evidence="ECO:0007829|PDB:6D5A"
FT TURN 336..338
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 339..343
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 360..363
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 365..374
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 380..385
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 387..389
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 392..394
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 399..401
FT /evidence="ECO:0007829|PDB:6D5A"
FT HELIX 404..408
FT /evidence="ECO:0007829|PDB:6D5A"
FT STRAND 411..413
FT /evidence="ECO:0007829|PDB:6D5A"
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
