PDAC_BACSU
ID PDAC_BACSU Reviewed; 467 AA.
AC O34798;
DT 25-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Peptidoglycan-N-acetylmuramic acid deacetylase PdaC;
DE Short=Peptidoglycan MurNAc deacetylase;
DE EC=3.5.1.-;
DE AltName: Full=Polysaccharide deacetylase PdaC;
GN Name=pdaC; Synonyms=yjeA; OrderedLocusNames=BSU12100;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9579062; DOI=10.1099/00221287-144-4-877;
RA Rivolta C., Soldo B., Lazarevic V., Joris B., Mauel C., Karamata D.;
RT "A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a
RT putative 12.3 kb operon involved in hexuronate catabolism and a perfectly
RT symmetrical hypothetical catabolite-responsive element.";
RL Microbiology 144:877-884(1998).
RN [2]
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 [3]
RP CAUTION.
RX PubMed=17878218; DOI=10.1093/jb/mvm177;
RA Ng K.L., Lam C.C., Fu Z., Han Y.F., Tsim K.W., Wong W.K.;
RT "Cloning and characterization of the yjeA gene, encoding a novel
RT deoxyribonuclease, from Bacillus subtilis.";
RL J. Biochem. 142:647-654(2007).
RN [4]
RP REPRESSION BY YYCFG.
RX PubMed=17581128; DOI=10.1111/j.1365-2958.2007.05782.x;
RA Bisicchia P., Noone D., Lioliou E., Howell A., Quigley S., Jensen T.,
RA Jarmer H., Devine K.M.;
RT "The essential YycFG two-component system controls cell wall metabolism in
RT Bacillus subtilis.";
RL Mol. Microbiol. 65:180-200(2007).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS,
RP ACTIVITY REGULATION, GENE NAME, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=22277649; DOI=10.1074/jbc.m111.329490;
RA Kobayashi K., Sudiarta I.P., Kodama T., Fukushima T., Ara K., Ozaki K.,
RA Sekiguchi J.;
RT "Identification and characterization of a novel polysaccharide deacetylase
RT C (PdaC) from Bacillus subtilis.";
RL J. Biol. Chem. 287:9765-9776(2012).
CC -!- FUNCTION: Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc)
CC residues in peptidoglycan, a modification that confers resistance to
CC lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc)
CC residues in peptidoglycan, but can deacylate chitin oligomers such as
CC GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan
CC (partially deacetylated GlcNAc polymer) and has very low activity
CC toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.
CC {ECO:0000269|PubMed:22277649}.
CC -!- ACTIVITY REGULATION: Activated by divalent metal cations; Mn(2+) is the
CC most efficient, followed by Ca(2+) and Mg(2+). In contrast to PgdA from
CC S.pneumoniae, these ions are not absolutely required for deacetylase
CC activity. {ECO:0000269|PubMed:22277649}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.8 mM for non-treated B.subtilis peptidoglycan
CC {ECO:0000269|PubMed:22277649};
CC KM=12.3 mM for GlcNAc4 {ECO:0000269|PubMed:22277649};
CC Note=kcat is 0.32 sec(-1) for the deacetylation of MurNAc residues in
CC peptidoglycan, and 0.24 sec(-1) for the deacetylation of GlcNAc4.;
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- INDUCTION: Negatively regulated by the two-component system YycFG.
CC {ECO:0000269|PubMed:17581128}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show sensitivity to
CC lysosyme, in contrast to wild-type. {ECO:0000269|PubMed:22277649}.
CC -!- MISCELLANEOUS: The product of deacetylated GlcNAc4 by PdaC is GlcNAc-
CC GlcNAc-GlcN-GlcNAc. {ECO:0000305|PubMed:22277649}.
CC -!- MISCELLANEOUS: Derepression of pdaC in cells depleted for yycFG leads
CC to increased resistance of the cell walls to lysozyme digestion.
CC -!- SIMILARITY: In the N-terminal section; belongs to the RsiV family.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the polysaccharide
CC deacetylase family. {ECO:0000305}.
CC -!- CAUTION: Was originally described as a deoxyribonuclease
CC (PubMed:17878218), but it was later shown that PdaC has no DNase
CC activity at all (PubMed:22277649). {ECO:0000305|PubMed:17878218,
CC ECO:0000305|PubMed:22277649}.
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DR EMBL; AF015825; AAC46306.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13067.1; -; Genomic_DNA.
DR PIR; G69849; G69849.
DR RefSeq; NP_389092.1; NC_000964.3.
DR RefSeq; WP_003245023.1; NZ_JNCM01000035.1.
DR PDB; 6H8L; X-ray; 1.54 A; A/B=270-467.
DR PDB; 6H8N; X-ray; 1.26 A; A/B=270-467.
DR PDBsum; 6H8L; -.
DR PDBsum; 6H8N; -.
DR AlphaFoldDB; O34798; -.
DR SMR; O34798; -.
DR IntAct; O34798; 2.
DR STRING; 224308.BSU12100; -.
DR PaxDb; O34798; -.
DR PRIDE; O34798; -.
DR EnsemblBacteria; CAB13067; CAB13067; BSU_12100.
DR GeneID; 936440; -.
DR KEGG; bsu:BSU12100; -.
DR PATRIC; fig|224308.179.peg.1307; -.
DR eggNOG; COG0726; Bacteria.
DR OMA; VQYYPET; -.
DR BioCyc; BSUB:BSU12100-MON; -.
DR Proteomes; UP000001570; 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:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR Gene3D; 3.90.640.20; -; 1.
DR InterPro; IPR021729; DUF3298.
DR InterPro; IPR011330; Glyco_hydro/deAcase_b/a-brl.
DR InterPro; IPR002509; NODB_dom.
DR InterPro; IPR025303; PdaC.
DR InterPro; IPR037126; PdaC/RsiV-like_sf.
DR InterPro; IPR017219; Peptidoglycan_deacetylase.
DR Pfam; PF11738; DUF3298; 1.
DR Pfam; PF13739; PdaC; 1.
DR Pfam; PF01522; Polysacc_deac_1; 1.
DR PIRSF; PIRSF037479; PG_GlcNAc_deacetylase; 1.
DR SUPFAM; SSF88713; SSF88713; 1.
DR PROSITE; PS51677; NODB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Hydrolase; Membrane; Metal-binding;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..467
FT /note="Peptidoglycan-N-acetylmuramic acid deacetylase PdaC"
FT /id="PRO_0000024846"
FT TRANSMEM 6..26
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 278..452
FT /note="NodB homology"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT ACT_SITE 285
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 427
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 286
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 336
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 340
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT SITE 401
FT /note="Raises pKa of active site His"
FT /evidence="ECO:0000250"
FT STRAND 279..286
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 290..303
FT /evidence="ECO:0007829|PDB:6H8N"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 313..318
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 320..328
FT /evidence="ECO:0007829|PDB:6H8N"
FT STRAND 332..335
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 343..345
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 348..366
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 376..378
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 382..388
FT /evidence="ECO:0007829|PDB:6H8N"
FT STRAND 390..392
FT /evidence="ECO:0007829|PDB:6H8N"
FT TURN 401..403
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 407..417
FT /evidence="ECO:0007829|PDB:6H8N"
FT STRAND 423..427
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 431..446
FT /evidence="ECO:0007829|PDB:6H8N"
FT HELIX 454..465
FT /evidence="ECO:0007829|PDB:6H8N"
SQ SEQUENCE 467 AA; 53839 MW; 95D2B1245968F804 CRC64;
MLAKRIKWFH VLIAVVCVVG LIGFFHNHSL KKETVMNKVR TDSQYGNVEI ATLVNDGKTF
NYAVNYPVFK NEKMDSALKR FAEKEVRQFQ KETKDVDQEH TTKRNELNVD YKIVHYAKQT
VAIVFNEYKY IGGAHGQTVK KTFNYDFSKQ AFLSIDDIFK EDADYLHKLS LIAYHELKKN
KDIAADDALL KEGTAPKKEN FSRFAIKEDY IELYFDTYQV AAGYLGEQSI AIKKSLLKDI
LKEQYIDKAK NKNKIKEQKP KHEVISLPKE ETVDPNQKVI ALTFDDGPNP ATTNQILDSL
KKYKGHATFF VLGSRVQYYP ETLIRMLKEG NEVGNHSWSH PLLTRLSVKE ALKQINDTQD
IIEKISGYRP TLVRPPYGGI NDELRSQMKM DVALWDVDPE DWKDRNKKTI VDRVMNQAGD
GRTILIHDIY RTSADAADEI IKKLTDQGYQ LVTVSQLEEV KKQREAK
