DAC_ACTSP
ID DAC_ACTSP Reviewed; 538 AA.
AC P39045;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=D-alanyl-D-alanine carboxypeptidase;
DE Short=DD-carboxypeptidase;
DE Short=DD-peptidase;
DE EC=3.4.16.4;
DE AltName: Full=Penicillin-binding protein;
DE Short=PBP;
DE Flags: Precursor;
GN Name=dac;
OS Actinomadura sp. (strain R39).
OC Bacteria; Actinobacteria; Streptosporangiales; Thermomonosporaceae;
OC Actinomadura; unclassified Actinomadura.
OX NCBI_TaxID=72570;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 50-87.
RX PubMed=1554361; DOI=10.1042/bj2820781;
RA Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O.,
RA van Beeumen J., Frere J.-M., Ghuysen J.-M.;
RT "Primary and predicted secondary structures of the Actinomadura R39
RT extracellular DD-peptidase, a penicillin-binding protein (PBP) related to
RT the Escherichia coli PBP4.";
RL Biochem. J. 282:781-788(1992).
RN [2]
RP ERRATUM OF PUBMED:1554361.
RX PubMed=1417760;
RA Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O.,
RA van Beeumen J., Frere J.-M., Ghuysen J.-M.;
RL Biochem. J. 286:981-982(1992).
RN [3]
RP PROTEIN SEQUENCE OF 95-101, AND SUBSTRATE-BINDING SITE.
RX PubMed=7305936; DOI=10.1042/bj1930083;
RA Duez C., Joris B., Frere J.-M., Ghuysen J.-M., van Beeumen J.;
RT "The penicillin-binding site in the exocellular DD-carboxypeptidase-
RT transpeptidase of Actinomadura R39.";
RL Biochem. J. 193:83-86(1981).
RN [4]
RP ACTIVITY REGULATION.
RX PubMed=11160090; DOI=10.1128/jb.183.5.1595-1599.2001;
RA Duez C., Vanhove M., Gallet X., Bouillenne F., Docquier J.-D., Brans A.,
RA Frere J.-M.;
RT "Purification and characterization of PBP4a, a new low-molecular-weight
RT penicillin-binding protein from Bacillus subtilis.";
RL J. Bacteriol. 183:1595-1599(2001).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 50-515 OF APOENZYME AND COMPLEX
RP WITH NITROCEFIN, AND PROCESSING OF C-TERMINUS.
RX PubMed=15987687; DOI=10.1074/jbc.m503271200;
RA Sauvage E., Herman R., Petrella S., Duez C., Bouillenne F., Frere J.-M.,
RA Charlier P.;
RT "Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains
RT in penicillin-binding proteins.";
RL J. Biol. Chem. 280:31249-31256(2005).
CC -!- FUNCTION: Removes C-terminal D-alanyl residues from sugar-peptide cell
CC wall precursors.
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 -!- ACTIVITY REGULATION: Inhibited by benzylpenicillin, cephaloridine,
CC ampicillin and cetiofur. {ECO:0000269|PubMed:11160090}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- SUBCELLULAR LOCATION: Secreted.
CC -!- SIMILARITY: Belongs to the peptidase S13 family. {ECO:0000305}.
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DR EMBL; X64790; CAA46023.1; -; Genomic_DNA.
DR PIR; S22409; S22409.
DR PDB; 1W79; X-ray; 1.80 A; A/B/C/D=50-538.
DR PDB; 1W8Q; X-ray; 2.85 A; A/B/C/D=50-538.
DR PDB; 1W8Y; X-ray; 2.40 A; A/B/C/D=50-538.
DR PDB; 2VGJ; X-ray; 2.40 A; A/B/C/D=50-538.
DR PDB; 2VGK; X-ray; 2.25 A; A/B/C/D=50-538.
DR PDB; 2WKE; X-ray; 2.20 A; A/B/C/D=50-515.
DR PDB; 2XDM; X-ray; 2.40 A; A/B/C/D=50-515.
DR PDB; 2XK1; X-ray; 2.80 A; A/B/C/D=50-515.
DR PDB; 2XLN; X-ray; 2.40 A; A/B/C/D=50-538.
DR PDB; 2Y4A; X-ray; 2.70 A; A/B/C/D=50-515.
DR PDB; 2Y55; X-ray; 2.60 A; A/B/C/D=50-515.
DR PDB; 2Y59; X-ray; 2.50 A; A/B/C/D=50-515.
DR PDB; 3ZCZ; X-ray; 2.60 A; A/B/C/D=50-516.
DR PDB; 3ZVT; X-ray; 3.10 A; A/B/C/D=50-515.
DR PDB; 3ZVW; X-ray; 2.00 A; A/B/C/D=50-515.
DR PDB; 4B4X; X-ray; 2.65 A; A/B/C/D=50-515.
DR PDB; 4B4Z; X-ray; 2.20 A; A/B/C/D=50-515.
DR PDB; 4BEN; X-ray; 2.15 A; A/B/C/D=50-515.
DR PDBsum; 1W79; -.
DR PDBsum; 1W8Q; -.
DR PDBsum; 1W8Y; -.
DR PDBsum; 2VGJ; -.
DR PDBsum; 2VGK; -.
DR PDBsum; 2WKE; -.
DR PDBsum; 2XDM; -.
DR PDBsum; 2XK1; -.
DR PDBsum; 2XLN; -.
DR PDBsum; 2Y4A; -.
DR PDBsum; 2Y55; -.
DR PDBsum; 2Y59; -.
DR PDBsum; 3ZCZ; -.
DR PDBsum; 3ZVT; -.
DR PDBsum; 3ZVW; -.
DR PDBsum; 4B4X; -.
DR PDBsum; 4B4Z; -.
DR PDBsum; 4BEN; -.
DR AlphaFoldDB; P39045; -.
DR SMR; P39045; -.
DR BindingDB; P39045; -.
DR ChEMBL; CHEMBL6016; -.
DR DrugBank; DB04742; (2R)-2-{(1R)-2-oxo-1-[(2-thienylacetyl)amino]ethyl}-5,6-dihydro-2h-1,3-thiazine-4-carboxylic acid.
DR MEROPS; S13.002; -.
DR BRENDA; 3.4.16.4; 129.
DR SABIO-RK; P39045; -.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P39045; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
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:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; -; 2.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR000667; Peptidase_S13.
DR PANTHER; PTHR30023; PTHR30023; 1.
DR Pfam; PF02113; Peptidase_S13; 1.
DR PRINTS; PR00922; DADACBPTASE3.
DR SUPFAM; SSF56601; SSF56601; 1.
DR TIGRFAMs; TIGR00666; PBP4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Carboxypeptidase; Cell shape;
KW Cell wall biogenesis/degradation; Direct protein sequencing; Hydrolase;
KW Peptidoglycan synthesis; Protease; Secreted; Signal.
FT SIGNAL 1..49
FT /evidence="ECO:0000269|PubMed:1554361"
FT CHAIN 50..515
FT /note="D-alanyl-D-alanine carboxypeptidase"
FT /id="PRO_0000027240"
FT PROPEP 516..538
FT /note="Removed in mature form"
FT /id="PRO_0000308945"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 146..319
FT /note="Absent in class-A beta-lactamases"
FT ACT_SITE 98
FT /note="Acyl-ester intermediate"
FT ACT_SITE 101
FT /note="Proton acceptor"
FT ACT_SITE 347
FT /evidence="ECO:0000250"
FT BINDING 459
FT /ligand="substrate"
FT CONFLICT 100..101
FT /note="MK -> GV (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 51..61
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:1W79"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 84..89
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 137..141
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:2Y4A"
FT HELIX 149..161
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:2VGJ"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:2Y4A"
FT TURN 208..211
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 212..221
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:1W79"
FT TURN 237..239
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 240..244
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 267..275
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 281..286
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 290..304
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 313..315
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 326..335
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 336..346
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 349..364
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 369..382
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 403..405
FT /evidence="ECO:0007829|PDB:2XDM"
FT HELIX 406..417
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 418..421
FT /evidence="ECO:0007829|PDB:2XK1"
FT HELIX 422..428
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 437..440
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 441..443
FT /evidence="ECO:0007829|PDB:1W79"
FT TURN 451..455
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 457..459
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 466..473
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 480..487
FT /evidence="ECO:0007829|PDB:1W79"
FT STRAND 490..492
FT /evidence="ECO:0007829|PDB:1W79"
FT HELIX 495..508
FT /evidence="ECO:0007829|PDB:1W79"
SQ SEQUENCE 538 AA; 54974 MW; 58A8300C32802E7B CRC64;
MKQSSPEPLR PRRTGGRGGA RRAAALVTIP LLPMTLLGAS PALADASGAR LTELREDIDA
ILEDPALEGA VSGVVVVDTA TGEELYSRDG GEQLLPASNM KLFTAAAALE VLGADHSFGT
EVAAESAPGR RGEVQDLYLV GRGDPTLSAE DLDAMAAEVA ASGVRTVRGD LYADDTWFDS
ERLVDDWWPE DEPYAYSAQI SALTVAHGER FDTGVTEVSV TPAAEGEPAD VDLGAAEGYA
ELDNRAVTGA AGSANTLVID RPVGTNTIAV TGSLPADAAP VTALRTVDEP AALAGHLFEE
ALESNGVTVK GDVGLGGVPA DWQDAEVLAD HTSAELSEIL VPFMKFSNNG HAEMLVKSIG
QETAGAGTWD AGLVGVEEAL SGLGVDTAGL VLNDGSGLSR GNLVTADTVV DLLGQAGSAP
WAQTWSASLP VAGESDPFVG GTLANRMRGT AAEGVVEAKT GTMSGVSALS GYVPGPEGEL
AFSIVNNGHS GPAPLAVQDA IAVRLAEYAG HQAPEGARMM RGPVQGSGEL ECSWVQAC
