DACB1_MYCTU
ID DACB1_MYCTU Reviewed; 405 AA.
AC O53380; F2GE74; I6XGW9; Q7D5P5;
DT 12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=D-alanyl-D-alanine carboxypeptidase DacB1 {ECO:0000305};
DE Short=D,D-carboxypeptidase DacB1 {ECO:0000303|PubMed:22906310};
DE Short=DD-carboxypeptidase {ECO:0000305};
DE Short=DD-peptidase {ECO:0000305};
DE EC=3.4.16.- {ECO:0000269|PubMed:22906310};
DE Flags: Precursor;
GN Name=dacB1 {ECO:0000303|PubMed:17286964};
GN OrderedLocusNames=Rv3330 {ECO:0000312|EMBL:CCP46151.1};
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 PHOSPHORYLATION AT THR-336, AND MUTAGENESIS OF THR-336.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17286964; DOI=10.1016/j.bbrc.2007.01.122;
RA Zheng X., Papavinasasundaram K.G., Av-Gay Y.;
RT "Novel substrates of Mycobacterium tuberculosis PknH Ser/Thr kinase.";
RL Biochem. Biophys. Res. Commun. 355:162-168(2007).
RN [3] {ECO:0007744|PubMed:21969609}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
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 [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=22906310; DOI=10.1111/j.1365-2958.2012.08199.x;
RA Kumar P., Arora K., Lloyd J.R., Lee I.Y., Nair V., Fischer E.,
RA Boshoff H.I., Barry C.E. III;
RT "Meropenem inhibits D,D-carboxypeptidase activity in Mycobacterium
RT tuberculosis.";
RL Mol. Microbiol. 86:367-381(2012).
RN [5] {ECO:0007744|PDB:4PPR}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 38-368 IN COMPLEX WITH MEROPENEM,
RP FUNCTION, ACTIVITY REGULATION, AND ACTIVE SITE.
RX PubMed=25551456; DOI=10.1371/journal.pone.0116249;
RA Prigozhin D.M., Krieger I.V., Huizar J.P., Mavrici D., Waldo G.S.,
RA Hung L.W., Sacchettini J.C., Terwilliger T.C., Alber T.;
RT "Subfamily-specific adaptations in the structures of two penicillin-binding
RT proteins from Mycobacterium tuberculosis.";
RL PLoS ONE 9:e116249-e116249(2014).
CC -!- FUNCTION: Probably cleaves the terminal D-Ala-D-Ala dipeptide of the
CC peptidoglycan stem peptide (Probable). Shows weak D,D-carboxypeptidase
CC activity in vitro (PubMed:22906310). Acts on the synthetic penta-
CC peptide substrate Penta-DAP (L-Ala-gamma-D-Gln-DAP-D-Ala-D-Ala)
CC (PubMed:22906310). The catalytic domain binds weakly to peptidoglycan
CC in vitro (PubMed:25551456). {ECO:0000269|PubMed:22906310,
CC ECO:0000269|PubMed:25551456, ECO:0000305|PubMed:22906310}.
CC -!- ACTIVITY REGULATION: Inhibited by the beta-lactam antibiotic meropenem.
CC {ECO:0000305|PubMed:25551456}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000255}.
CC -!- PTM: Phosphorylated on Thr-336 by PknH. {ECO:0000269|PubMed:17286964}.
CC -!- SIMILARITY: Belongs to the peptidase S11 family. {ECO:0000305}.
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DR EMBL; AL123456; CCP46151.1; -; Genomic_DNA.
DR RefSeq; NP_217847.1; NC_000962.3.
DR RefSeq; WP_003417415.1; NZ_NVQJ01000051.1.
DR PDB; 4PPR; X-ray; 2.00 A; A=38-368.
DR PDBsum; 4PPR; -.
DR AlphaFoldDB; O53380; -.
DR SMR; O53380; -.
DR STRING; 83332.Rv3330; -.
DR PaxDb; O53380; -.
DR PRIDE; O53380; -.
DR DNASU; 887607; -.
DR GeneID; 887607; -.
DR KEGG; mtu:Rv3330; -.
DR PATRIC; fig|83332.111.peg.3715; -.
DR TubercuList; Rv3330; -.
DR eggNOG; COG1686; Bacteria.
DR OMA; LIYQHAW; -.
DR PhylomeDB; O53380; -.
DR SABIO-RK; O53380; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IEA:InterPro.
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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR018044; Peptidase_S11.
DR InterPro; IPR001967; Peptidase_S11_N.
DR Pfam; PF00768; Peptidase_S11; 1.
DR PRINTS; PR00725; DADACBPTASE1.
DR SUPFAM; SSF56601; SSF56601; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carboxypeptidase; Cell membrane; Cell shape;
KW Cell wall biogenesis/degradation; Hydrolase; Membrane;
KW Peptidoglycan synthesis; Phosphoprotein; Protease; Reference proteome;
KW Signal; Transmembrane; Transmembrane helix.
FT SIGNAL 1..32
FT /evidence="ECO:0000255"
FT CHAIN 33..405
FT /note="D-alanyl-D-alanine carboxypeptidase DacB1"
FT /id="PRO_5010219484"
FT TRANSMEM 375..395
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ACT_SITE 121
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000305|PubMed:25551456"
FT ACT_SITE 124
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P0AEB2"
FT ACT_SITE 176
FT /evidence="ECO:0000250|UniProtKB:P0AEB2"
FT MOD_RES 336
FT /note="Phosphothreonine; by PknH"
FT /evidence="ECO:0000269|PubMed:17286964"
FT MUTAGEN 336
FT /note="T->A: 60% decrease in phosphorylation by PknH."
FT /evidence="ECO:0000269|PubMed:17286964"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 77..81
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 95..101
FT /evidence="ECO:0007829|PDB:4PPR"
FT TURN 102..104
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 106..112
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 124..134
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 162..164
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 165..174
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 191..204
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 227..238
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 241..247
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 263..266
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 270..274
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 278..286
FT /evidence="ECO:0007829|PDB:4PPR"
FT TURN 287..289
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 290..299
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 302..311
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 318..331
FT /evidence="ECO:0007829|PDB:4PPR"
FT STRAND 338..340
FT /evidence="ECO:0007829|PDB:4PPR"
FT HELIX 346..349
FT /evidence="ECO:0007829|PDB:4PPR"
SQ SEQUENCE 405 AA; 41682 MW; 9CD518E7C18EFF05 CRC64;
MAFLRSVSCL AAAVFAVGTG IGLPTAAGEP NAAPAACPYK VSTPPAVDSS EVPAAGEPPL
PLVVPPTPVG GNALGGCGII TAPGSAPAPG DVSAEAWLVA DLDSGAVIAA RDPHGRHRPA
SVIKVLVAMA SINTLTLNKS VAGTADDAAV EGTKVGVNTG GTYTVNQLLH GLLMHSGNDA
AYALARQLGG MPAALEKINL LAAKLGGRDT RVATPSGLDG PGMSTSAYDI GLFYRYAWQN
PVFADIVATR TFDFPGHGDH PGYELENDNQ LLYNYPGALG GKTGYTDDAG QTFVGAANRD
GRRLMTVLLH GTRQPIPPWE QAAHLLDYGF NTPAGTQIGT LIEPDPSLMS TDRNPADRQR
VDPQAAARIS AADALPVRVG VAVIGALIVF GLIMVARAMN RRPQH
