PDAA_BACSU
ID PDAA_BACSU Reviewed; 263 AA.
AC O34928;
DT 25-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Peptidoglycan-N-acetylmuramic acid deacetylase PdaA;
DE Short=Peptidoglycan MurNAc deacetylase;
DE EC=3.5.1.-;
DE Flags: Precursor;
GN Name=pdaA; Synonyms=yfjS; OrderedLocusNames=BSU07980;
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 / AC327;
RX PubMed=8969503; DOI=10.1099/13500872-142-11-3057;
RA Yamamoto H., Uchiyama S., Sekiguchi J.;
RT "Cloning and sequencing of a 40.6 kb segment in the 73 degrees-76 degrees
RT region of the Bacillus subtilis chromosome containing genes for trehalose
RT metabolism and acetoin utilization.";
RL Microbiology 142:3057-3065(1996).
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 FUNCTION, INDUCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=12374835; DOI=10.1128/jb.184.21.6007-6015.2002;
RA Fukushima T., Yamamoto H., Atrih A., Foster S.J., Sekiguchi J.;
RT "A polysaccharide deacetylase gene (pdaA) is required for germination and
RT for production of muramic delta-lactam residues in the spore cortex of
RT Bacillus subtilis.";
RL J. Bacteriol. 184:6007-6015(2002).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=14679227; DOI=10.1128/jb.186.1.80-89.2004;
RA Gilmore M.E., Bandyopadhyay D., Dean A.M., Linnstaedt S.D., Popham D.L.;
RT "Production of muramic delta-lactam in Bacillus subtilis spore
RT peptidoglycan.";
RL J. Bacteriol. 186:80-89(2004).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND PH DEPENDENCE.
RC STRAIN=168, and ATCC 6633 / PCI 219 / NRS 231;
RX PubMed=15687192; DOI=10.1128/jb.187.4.1287-1292.2005;
RA Fukushima T., Kitajima T., Sekiguchi J.;
RT "A polysaccharide deacetylase homologue, PdaA, in Bacillus subtilis acts as
RT an N-acetylmuramic acid deacetylase in vitro.";
RL J. Bacteriol. 187:1287-1292(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP N-ACETYLGLUCOSAMINE AND CADMIUM.
RX PubMed=15251431; DOI=10.1016/j.febslet.2004.06.013;
RA Blair D.E., van Aalten D.M.;
RT "Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase,
RT and a complex with N-acetyl-glucosamine.";
RL FEBS Lett. 570:13-19(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 24-263.
RG Northeast structural genomics consortium (NESG);
RT "Crystal structure of polysaccharide deacetylase (pdaa_bacsu) from B.
RT subtilis (pdaa_bacsu) Northeast structural genomics research consortium
RT (NESG) target sr127.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc)
CC residues in glycan strands of peptidoglycan, leading to the formation
CC of muramic delta-lactam residues in spore cortex, after
CC transpeptidation of deacetylated muramic acid residues. PdaA probably
CC carries out both deacetylation and lactam ring formation and requires
CC the product of CwlD activity on peptidoglycan as a substrate. Is
CC required for germination. Cannot use chitin oligomer (hexa-N-
CC acetylchitohexaose) as a substrate. {ECO:0000269|PubMed:12374835,
CC ECO:0000269|PubMed:14679227, ECO:0000269|PubMed:15687192}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:15687192};
CC -!- DEVELOPMENTAL STAGE: Expressed in the forespore, then exported into the
CC developing cortex. {ECO:0000269|PubMed:12374835}.
CC -!- INDUCTION: Expression is sigma G-dependent.
CC {ECO:0000269|PubMed:12374835}.
CC -!- DISRUPTION PHENOTYPE: Spores have no muramic delta-lactam structure in
CC the cortex and cannot germinate. Mutant spore peptidoglycan possesses
CC many MurNAc residues lacking peptide side chains.
CC {ECO:0000269|PubMed:12374835, ECO:0000269|PubMed:14679227}.
CC -!- MISCELLANEOUS: CwlD and PdaA are necessary and sufficient for muramic
CC delta-lactam production in B.subtilis spore peptidoglycan.
CC {ECO:0000305|PubMed:14679227}.
CC -!- SIMILARITY: Belongs to the polysaccharide deacetylase family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; D83967; BAA23389.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12627.1; -; Genomic_DNA.
DR PIR; B69807; B69807.
DR RefSeq; NP_388679.1; NC_000964.3.
DR RefSeq; WP_003244439.1; NZ_JNCM01000032.1.
DR PDB; 1NY1; X-ray; 1.80 A; A/B=24-263.
DR PDB; 1W17; X-ray; 1.90 A; A/B=1-263.
DR PDB; 1W1A; X-ray; 2.25 A; 1/2=12-263.
DR PDB; 1W1B; X-ray; 2.10 A; 1/2=12-263.
DR PDBsum; 1NY1; -.
DR PDBsum; 1W17; -.
DR PDBsum; 1W1A; -.
DR PDBsum; 1W1B; -.
DR AlphaFoldDB; O34928; -.
DR SMR; O34928; -.
DR STRING; 224308.BSU07980; -.
DR DrugBank; DB03740; N-acetyl-alpha-D-glucosamine.
DR PaxDb; O34928; -.
DR PRIDE; O34928; -.
DR EnsemblBacteria; CAB12627; CAB12627; BSU_07980.
DR GeneID; 936136; -.
DR KEGG; bsu:BSU07980; -.
DR PATRIC; fig|224308.179.peg.863; -.
DR eggNOG; COG0726; Bacteria.
DR InParanoid; O34928; -.
DR OMA; GNHSYHH; -.
DR PhylomeDB; O34928; -.
DR BioCyc; BSUB:BSU07980-MON; -.
DR BioCyc; MetaCyc:BSU07980-MON; -.
DR EvolutionaryTrace; O34928; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0019213; F:deacetylase activity; IDA:CACAO.
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 GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR CDD; cd10948; CE4_BsPdaA_like; 1.
DR InterPro; IPR011330; Glyco_hydro/deAcase_b/a-brl.
DR InterPro; IPR002509; NODB_dom.
DR InterPro; IPR014235; Spore_PdaA.
DR PANTHER; PTHR10587:SF78; PTHR10587:SF78; 1.
DR Pfam; PF01522; Polysacc_deac_1; 1.
DR SUPFAM; SSF88713; SSF88713; 1.
DR TIGRFAMs; TIGR02884; spore_pdaA; 1.
DR PROSITE; PS51677; NODB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Hydrolase; Metal-binding;
KW Reference proteome; Signal; Sporulation.
FT SIGNAL 1..23
FT /evidence="ECO:0000255"
FT CHAIN 24..263
FT /note="Peptidoglycan-N-acetylmuramic acid deacetylase PdaA"
FT /id="PRO_0000024842"
FT DOMAIN 66..247
FT /note="NodB homology"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT ACT_SITE 73
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 222
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 124
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT BINDING 128
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT SITE 193
FT /note="Raises pKa of active site His"
FT /evidence="ECO:0000250"
FT HELIX 46..54
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 65..76
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 81..90
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 101..106
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 108..116
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 136..154
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 165..167
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 171..179
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 217..221
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 228..242
FT /evidence="ECO:0007829|PDB:1NY1"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:1NY1"
FT HELIX 249..257
FT /evidence="ECO:0007829|PDB:1NY1"
SQ SEQUENCE 263 AA; 30069 MW; FEA2251646D169A0 CRC64;
MKWMCSICCA AVLLAGGAAQ AEAVPNEPIN WGFKRSVNHQ PPDAGKQLNS LIEKYDAFYL
GNTKEKTIYL TFDNGYENGY TPKVLDVLKK HRVTGTFFVT GHFVKDQPQL IKRMSDEGHI
IGNHSFHHPD LTTKTADQIQ DELDSVNEEV YKITGKQDNL YLRPPRGVFS EYVLKETKRL
GYQTVFWSVA FVDWKINNQK GKKYAYDHMI KQAHPGAIYL LHTVSRDNAE ALDDAITDLK
KQGYTFKSID DLMFEKEMRL PSL
