DACB_BACSU
ID DACB_BACSU Reviewed; 382 AA.
AC P35150;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=D-alanyl-D-alanine carboxypeptidase DacB {ECO:0000303|PubMed:1548223};
DE Short=DD-carboxypeptidase {ECO:0000303|PubMed:3933484};
DE Short=DD-peptidase;
DE EC=3.4.16.4 {ECO:0000305|PubMed:3933484};
DE AltName: Full=Penicillin-binding protein 5* {ECO:0000303|PubMed:3080407};
DE Short=PBP-5* {ECO:0000303|PubMed:3080407};
DE AltName: Full=Penicillin-binding protein 5a {ECO:0000303|PubMed:3933484};
DE Short=PBP-5a {ECO:0000303|PubMed:3933484};
DE Flags: Precursor;
GN Name=dacB {ECO:0000303|PubMed:1548223}; OrderedLocusNames=BSU23190;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 28-44.
RC STRAIN=168;
RX PubMed=1548223; DOI=10.1128/jb.174.6.1717-1725.1992;
RA Buchanan C.E., Ling M.-L.;
RT "Isolation and sequence analysis of dacB, which encodes a sporulation-
RT specific penicillin-binding protein in Bacillus subtilis.";
RL J. Bacteriol. 174:1717-1725(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=7934829; DOI=10.1111/j.1365-2958.1993.tb02670.x;
RA Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.;
RT "The organization of the Bacillus subtilis 168 chromosome region between
RT the spoVA and serA genetic loci, based on sequence data.";
RL Mol. Microbiol. 10:385-395(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION,
RP DEVELOPMENTAL STAGE, AND PENICILLIN-BINDING.
RC STRAIN=168;
RX PubMed=3933484; DOI=10.1042/bj2300825;
RA Todd J.A., Bone E.J., Ellar D.J.;
RT "The sporulation-specific penicillin-binding protein 5a from Bacillus
RT subtilis is a DD-carboxypeptidase in vitro.";
RL Biochem. J. 230:825-828(1985).
RN [5]
RP SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND PENICILLIN-BINDING.
RC STRAIN=168;
RX PubMed=3080407; DOI=10.1128/jb.165.2.498-503.1986;
RA Buchanan C.E., Neyman S.L.;
RT "Correlation of penicillin-binding protein composition with different
RT functions of two membranes in Bacillus subtilis forespores.";
RL J. Bacteriol. 165:498-503(1986).
RN [6] {ECO:0007744|PDB:3MFD}
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 27-358.
RA Cuff M.E., Rakowski E., Buck K., Joachimiak A.;
RT "The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-
RT alanine carboxypeptidase from Bacillus subtilis.";
RL Submitted (APR-2010) to the PDB data bank.
CC -!- FUNCTION: Removes C-terminal D-alanyl residues from sugar-peptide cell
CC wall precursors (PubMed:3933484). Required specifically for the
CC synthesis of the spore form of peptidoglycan (cortex) (Probable).
CC {ECO:0000269|PubMed:3933484, ECO:0000305|PubMed:3080407}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also
CC transpeptidation of peptidyl-alanyl moieties that are N-acyl
CC substituents of D-alanine.; EC=3.4.16.4;
CC Evidence={ECO:0000305|PubMed:3933484};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7-8.5. {ECO:0000269|PubMed:3933484};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- SUBCELLULAR LOCATION: Forespore outer membrane
CC {ECO:0000269|PubMed:3080407, ECO:0000269|PubMed:3933484}; Peripheral
CC membrane protein.
CC -!- DEVELOPMENTAL STAGE: Expressed at about stage III of sporulation.
CC Specifically enriched in stage IV forespores but not in stage IV mother
CC cells (PubMed:3933484, PubMed:3080407). {ECO:0000269|PubMed:3080407,
CC ECO:0000269|PubMed:3933484}.
CC -!- SIMILARITY: Belongs to the peptidase S11 family. {ECO:0000305}.
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DR EMBL; M84227; AAA22377.1; -; Genomic_DNA.
DR EMBL; L09228; AAA67490.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14251.1; -; Genomic_DNA.
DR PIR; S45552; S45552.
DR RefSeq; NP_390200.1; NC_000964.3.
DR RefSeq; WP_003230505.1; NZ_JNCM01000036.1.
DR PDB; 3MFD; X-ray; 1.75 A; A/B=27-358.
DR PDBsum; 3MFD; -.
DR AlphaFoldDB; P35150; -.
DR SMR; P35150; -.
DR STRING; 224308.BSU23190; -.
DR MEROPS; S11.004; -.
DR PaxDb; P35150; -.
DR PRIDE; P35150; -.
DR DNASU; 938953; -.
DR EnsemblBacteria; CAB14251; CAB14251; BSU_23190.
DR GeneID; 938953; -.
DR KEGG; bsu:BSU23190; -.
DR PATRIC; fig|224308.179.peg.2526; -.
DR eggNOG; COG1686; Bacteria.
DR InParanoid; P35150; -.
DR OMA; IQAGSWV; -.
DR PhylomeDB; P35150; -.
DR BioCyc; BSUB:BSU23190-MON; -.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P35150; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
DR GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IEA:UniProtKB-EC.
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 GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR018044; Peptidase_S11.
DR InterPro; IPR012907; Peptidase_S11_C.
DR InterPro; IPR001967; Peptidase_S11_N.
DR Pfam; PF07943; PBP5_C; 1.
DR Pfam; PF00768; Peptidase_S11; 1.
DR PRINTS; PR00725; DADACBPTASE1.
DR SMART; SM00936; PBP5_C; 1.
DR SUPFAM; SSF56601; SSF56601; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carboxypeptidase; Cell shape;
KW Cell wall biogenesis/degradation; Direct protein sequencing; Hydrolase;
KW Membrane; Peptidoglycan synthesis; Protease; Reference proteome; Signal;
KW Sporulation.
FT SIGNAL 1..27
FT /evidence="ECO:0000269|PubMed:1548223"
FT CHAIN 28..382
FT /note="D-alanyl-D-alanine carboxypeptidase DacB"
FT /id="PRO_0000027229"
FT ACT_SITE 60
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 63
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 115
FT /evidence="ECO:0000250"
FT BINDING 220
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT CONFLICT 179..194
FT /note="MKLKDYQKISGTKIYK -> IEAERLSKDFRHKNIQ (in Ref. 1; AA
FT sequence)"
FT /evidence="ECO:0000305"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:3MFD"
FT TURN 41..43
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 63..72
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 84..88
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 104..114
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 117..128
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 131..145
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 168..178
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 182..188
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 207..210
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 216..224
FT /evidence="ECO:0007829|PDB:3MFD"
FT TURN 225..227
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 228..237
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 240..248
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 252..266
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 267..273
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 275..277
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:3MFD"
FT TURN 285..289
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 290..294
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 296..301
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 302..305
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 308..314
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 320..323
FT /evidence="ECO:0007829|PDB:3MFD"
FT HELIX 325..327
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 330..339
FT /evidence="ECO:0007829|PDB:3MFD"
FT STRAND 342..351
FT /evidence="ECO:0007829|PDB:3MFD"
SQ SEQUENCE 382 AA; 43081 MW; 484D89F785A092DB CRC64;
MRIFKKAVFV IMISFLIATV NVNTAHAAID VSAKSAIIID GASGRVLYAK DEHQKRRIAS
ITKIMTAVLA IESGKMDQTV TVSANAVRTE GSAIYLTEGQ KVKLKDLVYG LMLRSGNDAA
VAIAEHVGGS LDGFVYMMNQ KAEQLGMKNT RFQNPHGLDD HENHYSTAYD MAILTKYAMK
LKDYQKISGT KIYKAETMES VWKNKNKLLT MLYPYSTGGK TGYTKLAKRT LVSTASKDGI
DLIAVTINDP NDWDDHMKMF NYVFEHYQTY LIAKKGDIPK LKGTFYESKA FIKRDITYLL
TEEEKENVKI NTTLLKPKKA WEKDASKIPD IVGHMEIMFN DATIAKVPIY YENERHQKPK
KQFFETFKSI FLNAAGGAKW SI
