PGDAE_HELPY
ID PGDAE_HELPY Reviewed; 293 AA.
AC O25080;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=Peptidoglycan deacetylase;
DE Short=PG deacetylase;
DE EC=3.5.1.-;
DE AltName: Full=Acetylxylan esterase;
DE EC=3.1.1.72;
GN Name=pgdA; OrderedLocusNames=HP_0310, C694_01565;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RA Manolov A., Prihodko E., Larin A., Karpova I., Semashko T., Alexeev D.,
RA Kostrjukova E., Govorun V.;
RT "Draft genome of Helicobacter pylori.";
RL Submitted (OCT-2012) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE OF 2-9, FUNCTION AS A PG DEACETYLASE, INDUCTION, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 43504 / NCTC 11637 / JCM 7653 / RPH 13487;
RX PubMed=19147492; DOI=10.1074/jbc.m808071200;
RA Wang G., Olczak A., Forsberg L.S., Maier R.J.;
RT "Oxidative stress-induced peptidoglycan deacetylase in Helicobacter
RT pylori.";
RL J. Biol. Chem. 284:6790-6800(2009).
RN [4]
RP FUNCTION, GENE NAME, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=B128, and X47;
RX PubMed=20805339; DOI=10.1128/iai.00307-10;
RA Wang G., Maier S.E., Lo L.F., Maier G., Dosi S., Maier R.J.;
RT "Peptidoglycan deacetylation in Helicobacter pylori contributes to
RT bacterial survival by mitigating host immune responses.";
RL Infect. Immun. 78:4660-4666(2010).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700392 / 26695, and X47;
RX PubMed=23221800; DOI=10.1128/mbio.00409-12;
RA Wang G., Lo L.F., Forsberg L.S., Maier R.J.;
RT "Helicobacter pylori peptidoglycan modifications confer lysozyme resistance
RT and contribute to survival in the host.";
RL MBio 3:E00409-E00412(2012).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION AS AN ACETYLXYLAN ESTERASE,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=23825549; DOI=10.1371/journal.pone.0066605;
RA Choi H.P., Juarez S., Ciordia S., Fernandez M., Bargiela R., Albar J.P.,
RA Mazumdar V., Anton B.P., Kasif S., Ferrer M., Steffen M.;
RT "Biochemical characterization of hypothetical proteins from Helicobacter
RT pylori.";
RL PLoS ONE 8:E66605-E66605(2013).
CC -!- FUNCTION: Catalyzes the N-deacetylation of peptidoglycan (PG), an
CC important mechanism that appears to confer lysozyme resistance and to
CC mitigate host immune detection; this likely contributes to pathogen
CC persistence in the host. The exact nature of the residue in PG that is
CC deacetylated has not been determined. Is also able to catalyze the
CC deacetylation of acetylated xylan, and, to a lesser extent, that of
CC chitin and chitosan. Therefore, this enzyme might play a role during
CC infection, considering that xylan-containing carbohydrate structures
CC are among those commonly consumed by humans.
CC {ECO:0000269|PubMed:19147492, ECO:0000269|PubMed:20805339,
CC ECO:0000269|PubMed:23221800, ECO:0000269|PubMed:23825549}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Deacetylation of xylans and xylo-oligosaccharides.;
CC EC=3.1.1.72; Evidence={ECO:0000269|PubMed:23825549};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.85 mM for chitin {ECO:0000269|PubMed:23825549};
CC KM=0.85 mM for chitosan {ECO:0000269|PubMed:23825549};
CC KM=0.42 mM for acetylated xylan {ECO:0000269|PubMed:23825549};
CC KM=0.18 mM for pNP-acetate {ECO:0000269|PubMed:23825549};
CC Note=kcat is 775 min(-1), 968 min(-1), 2549 min(-1) and 1029 min(-1)
CC with chitin, chitosan, acetylated xylan, and pNP-acetate as
CC substrate, respectively.;
CC pH dependence:
CC Optimum pH is 6.0 with acetylated xylan as substrate. Is active at
CC acidic pH ranging from 5.0 to 6.0. {ECO:0000269|PubMed:23825549};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius with acetylated xylan as
CC substrate. Retains about 80% of the activity at 30-55 degrees
CC Celsius. {ECO:0000269|PubMed:23825549};
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- INDUCTION: Its expression is markedly up-regulated upon cell exposure
CC to oxidative stress. Is also significantly induced (3.5-fold) when
CC H.pylori cells are in contact with macrophages.
CC {ECO:0000269|PubMed:19147492, ECO:0000269|PubMed:20805339}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are considerably less
CC resistant to lysozyme than wild-type, and show an absence or
CC significantly reduced amount of N-deacetylated muropeptides in the
CC bacterial PG. Mutant strains also have attenuated ability to colonize
CC mouse stomachs, and induce a stronger immune response in the host.
CC Disruption of this gene does not affect oxidative stress resistance
CC characteristics, indicating that the major physiological role of the
CC enzyme is not in combating oxidative stress.
CC {ECO:0000269|PubMed:19147492, ECO:0000269|PubMed:20805339,
CC ECO:0000269|PubMed:23221800}.
CC -!- SIMILARITY: Belongs to the polysaccharide deacetylase family.
CC {ECO:0000305}.
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DR EMBL; AE000511; AAD07376.1; -; Genomic_DNA.
DR EMBL; CP003904; AFV41534.1; -; Genomic_DNA.
DR PIR; F64558; F64558.
DR RefSeq; NP_207108.1; NC_000915.1.
DR RefSeq; WP_001040419.1; NC_018939.1.
DR AlphaFoldDB; O25080; -.
DR SMR; O25080; -.
DR STRING; 85962.C694_01565; -.
DR PaxDb; O25080; -.
DR DNASU; 899203; -.
DR EnsemblBacteria; AAD07376; AAD07376; HP_0310.
DR KEGG; heo:C694_01565; -.
DR KEGG; hpy:HP_0310; -.
DR PATRIC; fig|85962.47.peg.330; -.
DR eggNOG; COG0726; Bacteria.
DR HOGENOM; CLU_029940_1_0_7; -.
DR OMA; HNDFTPY; -.
DR PhylomeDB; O25080; -.
DR BRENDA; 3.5.1.104; 2604.
DR SABIO-RK; O25080; -.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0046555; F:acetylxylan esterase activity; IEA:UniProtKB-EC.
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:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0045493; P:xylan catabolic process; IEA:UniProtKB-KW.
DR CDD; cd10938; CE4_HpPgdA_like; 1.
DR InterPro; IPR011330; Glyco_hydro/deAcase_b/a-brl.
DR InterPro; IPR002509; NODB_dom.
DR InterPro; IPR037950; PgdA-like.
DR Pfam; PF01522; Polysacc_deac_1; 1.
DR SUPFAM; SSF88713; SSF88713; 1.
DR PROSITE; PS51677; NODB; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Cell wall biogenesis/degradation;
KW Direct protein sequencing; Hydrolase; Metal-binding;
KW Polysaccharide degradation; Reference proteome; Stress response;
KW Xylan degradation; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:19147492"
FT CHAIN 2..293
FT /note="Peptidoglycan deacetylase"
FT /id="PRO_0000424438"
FT DOMAIN 29..276
FT /note="NodB homology"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT BINDING 14
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 86
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 90
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
SQ SEQUENCE 293 AA; 33677 MW; 42ADF39EE681532D CRC64;
MAKEILVAYG VDIDAVAGWL GSYGGEDSPD DISRGLFAGE VGIPRLLKLF KKYHLPATWF
SPGHSIETFS EQMKMIVDAG HEVGAHGYSH ENPIAMTAKQ EEDVLLKSVE LIKDLTGKAP
TGYVAPWWEF SNITNELLLK HGFKYDHSLM HNDFTPYYVR VGDSWSKIDY SLEAKDWMKP
LIRGVETDLV EIPANWYLDD LPPMMFIKKS PNSFGFVSPH DIGQMWIDQF DWVYREMDYA
VFSMTIHPDV SARPQVLLMH EKIIEHINKH EGVRWVTFNE IADDFLKRNP RKK
