LDT3_MYCTU
ID LDT3_MYCTU Reviewed; 271 AA.
AC O06825; F2GEW6; I6Y6I9; Q7D8G2;
DT 01-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 25-MAY-2022, entry version 114.
DE RecName: Full=Probable L,D-transpeptidase 3;
DE Short=LDT 3;
DE EC=2.3.2.-;
DE AltName: Full=Ldt(Mt3);
GN OrderedLocusNames=Rv1433, RVBD_1433; ORFNames=P425_01489;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RG The Broad Institute Genome Sequencing Platform;
RA Galagan J., Kreiswirth B., Dobos K., Fortune S., Fitzgerald M., Young S.K.,
RA Zeng Q., Gargeya S., Abouelleil A., Alvarado L., Berlin A.M., Chapman S.B.,
RA Gainer-Dewar J., Goldberg J., Gnerre S., Griggs A., Gujja S., Hansen M.,
RA Howarth C., Imamovic A., Larimer J., McCowan C., Murphy C., Pearson M.,
RA Poon T., Priest M., Roberts A., Saif S., Shea T., Sykes S., Wortman J.,
RA Nusbaum C., Birren B.;
RT "The genome sequence of Mycobacterium tuberculosis H37Rv.";
RL Submitted (NOV-2013) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RG The Broad Institute Genomics Platform;
RG The Broad Institute Genome Sequencing Center for Infectious Disease;
RA Earl A.M., Kreiswirth B., Gomez J., Victor T., Desjardins C., Abeel T.,
RA Young S., Zeng Q., Gargeya S., Abouelleil A., Alvarado L., Chapman S.B.,
RA Gainer-Dewar J., Goldberg J., Griggs A., Gujja S., Hansen M., Howarth C.,
RA Imamovic A., Larimer J., Murphy C., Naylor J., Pearson M., Poon T.W.,
RA Priest M., Roberts A., Saif S., Shea T., Sykes S., Wortman J., Nusbaum C.,
RA Birren B.;
RT "The genome sequence of Mycobacterium tuberculosis H37Rv.";
RL Submitted (APR-2014) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, AND ACTIVITY 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).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 20-271.
RC STRAIN=ATCC 25618 / H37Rv;
RG Midwest center for structural genomics (MCSG);
RT "X-ray crystal structure of an l,d-transpeptidase from Mycobacterium
RT tuberculosis H37Rv (casp target).";
RL Submitted (JUN-2013) to the PDB data bank.
CC -!- FUNCTION: Probable L,D-transpeptidase that may perform as-yet-unknown
CC cross-linking reactions in M.tuberculosis. Is not able to generate 3->3
CC cross-links in peptidoglycan, using tetrapeptide stems as acyl donor
CC substrates. May function in the anchoring of proteins to peptidoglycan.
CC {ECO:0000269|PubMed:24041897}.
CC -!- ACTIVITY REGULATION: Is irreversibly inactivated by the beta-lactams
CC carbapenems via the formation of a covalent adduct resulting from
CC enzyme acylation; imipenem is the most efficient drug for in vitro
CC LdtMt3 inactivation. {ECO:0000269|PubMed:24041897}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
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DR EMBL; CP003248; AFN49342.1; -; Genomic_DNA.
DR EMBL; AL123456; CCP44192.1; -; Genomic_DNA.
DR EMBL; JLDD01000016; KBJ35648.1; -; Genomic_DNA.
DR RefSeq; NP_215949.1; NC_000962.3.
DR RefSeq; WP_003407384.1; NZ_NVQJ01000038.1.
DR PDB; 4K73; X-ray; 1.65 A; A=20-271.
DR PDB; 6D4K; X-ray; 1.32 A; A=32-271.
DR PDB; 6D51; X-ray; 1.83 A; A=33-271.
DR PDBsum; 4K73; -.
DR PDBsum; 6D4K; -.
DR PDBsum; 6D51; -.
DR AlphaFoldDB; O06825; -.
DR SMR; O06825; -.
DR STRING; 83332.Rv1433; -.
DR PaxDb; O06825; -.
DR DNASU; 886649; -.
DR GeneID; 45425411; -.
DR GeneID; 886649; -.
DR KEGG; mtu:Rv1433; -.
DR KEGG; mtv:RVBD_1433; -.
DR TubercuList; Rv1433; -.
DR eggNOG; COG1376; Bacteria.
DR OMA; HSAPWAV; -.
DR PhylomeDB; O06825; -.
DR BRENDA; 2.3.2.B14; 3445.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001584; Chromosome.
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..271
FT /note="Probable L,D-transpeptidase 3"
FT /id="PRO_0000430335"
FT DOMAIN 167..269
FT /note="YkuD"
FT ACT_SITE 228
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 246
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT SITE 246
FT /note="Binds to carbapenem drug (covalent)"
FT /evidence="ECO:0000250"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 55..61
FT /evidence="ECO:0007829|PDB:6D4K"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:6D4K"
FT HELIX 69..75
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 86..92
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 95..102
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 109..114
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:6D4K"
FT TURN 133..136
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 182..185
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 188..196
FT /evidence="ECO:0007829|PDB:6D4K"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 211..219
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:6D4K"
FT HELIX 231..236
FT /evidence="ECO:0007829|PDB:6D4K"
FT TURN 237..239
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:6D4K"
FT HELIX 251..260
FT /evidence="ECO:0007829|PDB:6D4K"
FT STRAND 266..270
FT /evidence="ECO:0007829|PDB:6D4K"
SQ SEQUENCE 271 AA; 28701 MW; 719301725EAC509A CRC64;
MRAVFGCAIA VVGIAGSVVA GPADIHLVAA KQSYGFAVAS VLPTRGQVVG VAHPVVVTFS
APITNPANRH AAERAVEVKS TPAMTGKFEW LDNDVVQWVP DRFWPAHSTV ELSVGSLSSD
FKTGPAVVGV ASISQHTFTV SIDGVEEGPP PPLPAPHHRV HFGEDGVMPA SMGRPEYPTP
VGSYTVLSKE RSVIMDSSSV GIPVDDPDGY RLSVDYAVRI TSRGLYVHSA PWALPALGLE
NVSHGCISLS REDAEWYYNA VDIGDPVIVQ E
