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D-alanyl-D-alanine carboxypeptidase DacB (DD-carboxypeptidase) (DD-peptidase) (EC 3.4.16.4) (D-alanyl-D-alanine endopeptidase) (DD-endopeptidase) (EC 3.4.21.-) (Penicillin-binding protein 4) (PBP-4)

 DACB_ECOLI              Reviewed;         477 AA.
P24228; Q2M930;
01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
01-NOV-1995, sequence version 2.
28-MAR-2018, entry version 147.
RecName: Full=D-alanyl-D-alanine carboxypeptidase DacB;
Short=DD-carboxypeptidase;
Short=DD-peptidase;
EC=3.4.16.4;
AltName: Full=D-alanyl-D-alanine endopeptidase;
Short=DD-endopeptidase;
EC=3.4.21.-;
AltName: Full=Penicillin-binding protein 4;
Short=PBP-4;
Flags: Precursor;
Name=dacB; OrderedLocusNames=b3182, JW3149;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 21-31.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=2040429; DOI=10.1016/0378-1097(91)90160-C;
Mottl H., Terpstra P., Keck W.;
"Penicillin-binding protein 4 of Escherichia coli shows a novel type
of primary structure among penicillin-interacting proteins.";
FEMS Microbiol. Lett. 62:213-220(1991).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
Wang R., Kushner S.R.;
Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND X-RAY CRYSTALLOGRAPHY
(1.55 ANGSTROMS) OF 21-477 OF APOENZYME AND IN COMPLEX WITH PENICILLIN
ANTIBIOTICS.
STRAIN=K12;
PubMed=16411754; DOI=10.1021/bi051533t;
Kishida H., Unzai S., Roper D.I., Lloyd A., Park S.-Y., Tame J.R.H.;
"Crystal structure of penicillin binding protein 4 (dacB) from
Escherichia coli, both in the native form and covalently linked to
various antibiotics.";
Biochemistry 45:783-792(2006).
[6]
FUNCTION.
PubMed=2046551; DOI=10.1111/j.1365-2958.1991.tb00739.x;
Korat B., Mottl H., Keck W.;
"Penicillin-binding protein 4 of Escherichia coli: molecular cloning
of the dacB gene, controlled overexpression, and alterations in murein
composition.";
Mol. Microbiol. 5:675-684(1991).
-!- FUNCTION: Not involved in transpeptidation but exclusively
catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.
{ECO:0000269|PubMed:2046551}.
-!- CATALYTIC ACTIVITY: Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-
D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are
N-acyl substituents of D-alanine.
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
-!- INTERACTION:
P0A6E4:argG; NbExp=2; IntAct=EBI-1131834, EBI-1120296;
-!- SUBCELLULAR LOCATION: Periplasm {ECO:0000305}.
-!- MISCELLANEOUS: In E.coli there are three murein endopeptidases:
two are penicillin sensitive (DacB and PbpG), the other (MepA)
not.
-!- SIMILARITY: Belongs to the peptidase S13 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X59460; CAA42070.1; -; Genomic_DNA.
EMBL; X60038; CAA42643.1; -; Genomic_DNA.
EMBL; U01376; AAA97505.1; -; Genomic_DNA.
EMBL; U18997; AAA57983.1; -; Genomic_DNA.
EMBL; U00096; AAC76214.1; -; Genomic_DNA.
EMBL; AP009048; BAE77226.1; -; Genomic_DNA.
PIR; A54535; A54535.
RefSeq; NP_417649.1; NC_000913.3.
RefSeq; WP_001212619.1; NZ_CP014272.1.
PDB; 2EX2; X-ray; 1.55 A; A=21-477.
PDB; 2EX6; X-ray; 1.60 A; A=21-477.
PDB; 2EX8; X-ray; 1.60 A; A=21-477.
PDB; 2EX9; X-ray; 1.65 A; A=21-477.
PDB; 2EXA; X-ray; 1.70 A; A=21-477.
PDB; 2EXB; X-ray; 1.75 A; A=21-477.
PDBsum; 2EX2; -.
PDBsum; 2EX6; -.
PDBsum; 2EX8; -.
PDBsum; 2EX9; -.
PDBsum; 2EXA; -.
PDBsum; 2EXB; -.
ProteinModelPortal; P24228; -.
SMR; P24228; -.
BioGrid; 4262437; 332.
IntAct; P24228; 1.
STRING; 316385.ECDH10B_3356; -.
ChEMBL; CHEMBL2354204; -.
DrugBank; DB01328; Cefonicid.
DrugBank; DB01329; Cefoperazone.
DrugBank; DB01331; Cefoxitin.
DrugBank; DB00303; Ertapenem.
DrugBank; DB04570; Latamoxef.
DrugBank; DB00760; Meropenem.
DrugBank; DB00417; Phenoxymethylpenicillin.
MEROPS; S13.001; -.
MoonProt; P24228; -.
PaxDb; P24228; -.
PRIDE; P24228; -.
EnsemblBacteria; AAC76214; AAC76214; b3182.
EnsemblBacteria; BAE77226; BAE77226; BAE77226.
GeneID; 947693; -.
KEGG; ecj:JW3149; -.
KEGG; eco:b3182; -.
PATRIC; fig|511145.12.peg.3275; -.
EchoBASE; EB0198; -.
EcoGene; EG10202; dacB.
eggNOG; ENOG4106HRJ; Bacteria.
eggNOG; COG2027; LUCA.
HOGENOM; HOG000279266; -.
InParanoid; P24228; -.
KO; K07259; -.
OMA; DGTMRKR; -.
PhylomeDB; P24228; -.
BioCyc; EcoCyc:EG10202-MONOMER; -.
BioCyc; MetaCyc:EG10202-MONOMER; -.
BRENDA; 3.4.16.4; 2165.
BRENDA; 3.4.17.14; 2026.
UniPathway; UPA00219; -.
EvolutionaryTrace; P24228; -.
PRO; PR:P24228; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0030288; C:outer membrane-bounded periplasmic space; IMP:EcoliWiki.
GO; GO:0004180; F:carboxypeptidase activity; IMP:EcoCyc.
GO; GO:0004175; F:endopeptidase activity; IDA:EcoCyc.
GO; GO:0008658; F:penicillin binding; IDA:EcoCyc.
GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IMP:EcoliWiki.
GO; GO:0016998; P:cell wall macromolecule catabolic process; IDA:EcoCyc.
GO; GO:0071555; P:cell wall organization; IDA:EcoCyc.
GO; GO:0043093; P:FtsZ-dependent cytokinesis; IGI:EcoCyc.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0009253; P:peptidoglycan catabolic process; IDA:EcoCyc.
GO; GO:0000270; P:peptidoglycan metabolic process; IDA:EcoCyc.
GO; GO:0009254; P:peptidoglycan turnover; IDA:EcoCyc.
GO; GO:0008360; P:regulation of cell shape; IGI:EcoCyc.
GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
InterPro; IPR012338; Beta-lactam/transpept-like.
InterPro; IPR000667; Peptidase_S13.
PANTHER; PTHR30023; PTHR30023; 1.
Pfam; PF02113; Peptidase_S13; 1.
PRINTS; PR00922; DADACBPTASE3.
SUPFAM; SSF56601; SSF56601; 1.
TIGRFAMs; TIGR00666; PBP4; 1.
1: Evidence at protein level;
3D-structure; Antibiotic resistance; Cell cycle; Cell division;
Cell shape; Cell wall biogenesis/degradation; Complete proteome;
Direct protein sequencing; Hydrolase; Peptidoglycan synthesis;
Periplasm; Reference proteome; Signal.
SIGNAL 1 20 {ECO:0000269|PubMed:2040429}.
CHAIN 21 477 D-alanyl-D-alanine carboxypeptidase DacB.
/FTId=PRO_0000027241.
REGION 90 263 Absent in class-A beta-lactamases.
ACT_SITE 62 62 Acyl-ester intermediate.
ACT_SITE 65 65 Proton acceptor. {ECO:0000250}.
ACT_SITE 306 306 {ECO:0000250}.
BINDING 417 417 Substrate. {ECO:0000250}.
CONFLICT 261 261 D -> Y (in Ref. 5). {ECO:0000305}.
CONFLICT 427 427 L -> Q (in Ref. 1; CAA42643).
{ECO:0000305}.
HELIX 23 27 {ECO:0000244|PDB:2EX2}.
STRAND 35 42 {ECO:0000244|PDB:2EX2}.
STRAND 49 53 {ECO:0000244|PDB:2EX2}.
HELIX 61 63 {ECO:0000244|PDB:2EX2}.
HELIX 64 75 {ECO:0000244|PDB:2EX2}.
STRAND 83 93 {ECO:0000244|PDB:2EX2}.
STRAND 96 104 {ECO:0000244|PDB:2EX2}.
HELIX 113 125 {ECO:0000244|PDB:2EX2}.
STRAND 130 133 {ECO:0000244|PDB:2EX2}.
STRAND 135 138 {ECO:0000244|PDB:2EX2}.
HELIX 153 155 {ECO:0000244|PDB:2EX2}.
HELIX 159 161 {ECO:0000244|PDB:2EX2}.
HELIX 170 172 {ECO:0000244|PDB:2EX2}.
STRAND 173 179 {ECO:0000244|PDB:2EX2}.
STRAND 189 191 {ECO:0000244|PDB:2EX2}.
STRAND 199 207 {ECO:0000244|PDB:2EX2}.
STRAND 209 211 {ECO:0000244|PDB:2EX9}.
TURN 213 216 {ECO:0000244|PDB:2EX2}.
STRAND 219 224 {ECO:0000244|PDB:2EX2}.
HELIX 225 227 {ECO:0000244|PDB:2EX2}.
STRAND 228 236 {ECO:0000244|PDB:2EX2}.
STRAND 242 247 {ECO:0000244|PDB:2EX2}.
HELIX 251 265 {ECO:0000244|PDB:2EX2}.
STRAND 269 272 {ECO:0000244|PDB:2EX2}.
STRAND 274 277 {ECO:0000244|PDB:2EX2}.
STRAND 285 291 {ECO:0000244|PDB:2EX2}.
HELIX 295 305 {ECO:0000244|PDB:2EX2}.
HELIX 308 323 {ECO:0000244|PDB:2EX2}.
HELIX 329 342 {ECO:0000244|PDB:2EX2}.
STRAND 356 358 {ECO:0000244|PDB:2EX2}.
HELIX 367 379 {ECO:0000244|PDB:2EX2}.
HELIX 381 384 {ECO:0000244|PDB:2EX2}.
HELIX 387 389 {ECO:0000244|PDB:2EX2}.
TURN 393 395 {ECO:0000244|PDB:2EX2}.
HELIX 397 399 {ECO:0000244|PDB:2EX2}.
HELIX 403 407 {ECO:0000244|PDB:2EX2}.
TURN 411 413 {ECO:0000244|PDB:2EX2}.
STRAND 414 421 {ECO:0000244|PDB:2EX2}.
STRAND 424 432 {ECO:0000244|PDB:2EX2}.
STRAND 438 447 {ECO:0000244|PDB:2EX2}.
HELIX 452 454 {ECO:0000244|PDB:2EX2}.
TURN 455 457 {ECO:0000244|PDB:2EX6}.
HELIX 460 475 {ECO:0000244|PDB:2EX2}.
SEQUENCE 477 AA; 51798 MW; 4EF5E43D2BEC4E5B CRC64;
MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI DYHSQQMALP
ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD LVARFGADPT LKRQDIRNMV
ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS
APKPGDMAFI RVASYYPVTM FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE
PLPLAFAVQD GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK
IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN TIIADGSGLS
RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ YRAGLHQAGV DGKVSAKTGS
LQGVYNLAGF ITTASGQRMA FVQYLSGYAV EPADQRNRRI PLVRFESRLY KDIYQNN


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