PGDA1_BACCR
ID PGDA1_BACCR Reviewed; 275 AA.
AC Q81EK9;
DT 31-JUL-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Peptidoglycan-N-acetylglucosamine deacetylase BC_1960 {ECO:0000303|PubMed:15961396};
DE Short=Peptidoglycan GlcNAc deacetylase {ECO:0000303|PubMed:15961396};
DE EC=3.5.1.104 {ECO:0000269|PubMed:15961396, ECO:0000269|PubMed:29983281};
GN OrderedLocusNames=BC_1960 {ECO:0000312|EMBL:AAP08931.1};
OS Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC
OS 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=226900;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=12721630; DOI=10.1038/nature01582;
RA Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V.,
RA Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M.,
RA Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G.,
RA Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N.C.;
RT "Genome sequence of Bacillus cereus and comparative analysis with Bacillus
RT anthracis.";
RL Nature 423:87-91(2003).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=15961396; DOI=10.1074/jbc.m407426200;
RA Psylinakis E., Boneca I.G., Mavromatis K., Deli A., Hayhurst E.,
RA Foster S.J., Vaarum K.M., Bouriotis V.;
RT "Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus,
RT highly conserved proteins in Bacillus anthracis.";
RL J. Biol. Chem. 280:30856-30863(2005).
RN [3]
RP CRYSTALLIZATION.
RX PubMed=18323609; DOI=10.1107/s1744309108002510;
RA Tsalafouta A., Psylinakis E., Kapetaniou E.G., Kotsifaki D., Deli A.,
RA Roidis A., Bouriotis V., Kokkinidis M.;
RT "Purification, crystallization and preliminary X-ray analysis of the
RT peptidoglycan N-acetylglucosamine deacetylase BC1960 from Bacillus cereus
RT in the presence of its substrate (GlcNAc)6.";
RL Acta Crystallogr. F 64:203-205(2008).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=29983281; DOI=10.1016/j.bmc.2018.06.045;
RA Balomenou S., Koutsioulis D., Tomatsidou A., Tzanodaskalaki M.,
RA Petratos K., Bouriotis V.;
RT "Polysaccharide deacetylases serve as new targets for the design of
RT inhibitors against Bacillus anthracis and Bacillus cereus.";
RL Bioorg. Med. Chem. 26:3845-3851(2018).
RN [5] {ECO:0007744|PDB:4L1G}
RP X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) OF 9-275, HYDROXYLATION AT PRO-179,
RP AND ACTIVITY REGULATION.
RX PubMed=28333455; DOI=10.1021/jacs.6b12209;
RA Fadouloglou V.E., Balomenou S., Aivaliotis M., Kotsifaki D., Arnaouteli S.,
RA Tomatsidou A., Efstathiou G., Kountourakis N., Miliara S., Griniezaki M.,
RA Tsalafouta A., Pergantis S.A., Boneca I.G., Glykos N.M., Bouriotis V.,
RA Kokkinidis M.;
RT "Unusual alpha-carbon hydroxylation of proline promotes active-site
RT maturation.";
RL J. Am. Chem. Soc. 139:5330-5337(2017).
RN [6] {ECO:0007744|PDB:5O6Y}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 61-274 IN COMPLEX WITH ZINC, AND
RP COFACTOR.
RA Fadouloglou V.E., Kotsifaki D., Kokkinidis M.;
RT "Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine
RT deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide.";
RL Submitted (JUN-2017) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc)
CC residues in peptidoglycan (PubMed:15961396, PubMed:29983281). Also acts
CC on soluble chitin substrates and N-acetylchitooligomers. Acts on cell
CC wall peptidoglycan from the Gram-positive bacteria B.cereus and
CC B.subtilis and the Gram-negative bacterium H.pylori. Not active on
CC acetylated xylan (PubMed:15961396). {ECO:0000269|PubMed:15961396,
CC ECO:0000269|PubMed:29983281}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=peptidoglycan-N-acetyl-D-glucosamine + H2O = peptidoglycan-D-
CC glucosamine + acetate.; EC=3.5.1.104;
CC Evidence={ECO:0000269|PubMed:15961396, ECO:0000269|PubMed:29983281};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000269|Ref.6};
CC -!- ACTIVITY REGULATION: Deacetylase activity is stimulated by
CC hydroxylation on Pro-179 (PubMed:28333455). Inhibited by CuCl(2) and
CC ZnCl(2) (PubMed:15961396). Inhibited by the hydroxamate N-hydroxy-4-
CC (naphthalene-1-yl)benzamide (NHNB) (PubMed:29983281).
CC {ECO:0000269|PubMed:15961396, ECO:0000269|PubMed:28333455,
CC ECO:0000269|PubMed:29983281}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.1 mM for GlcNAc(2) {ECO:0000269|PubMed:15961396};
CC KM=2.46 mM for GlcNAc(3) {ECO:0000269|PubMed:15961396};
CC KM=1.18 mM for GlcNAc(4) {ECO:0000269|PubMed:15961396};
CC KM=0.37 mM for GlcNAc(5) {ECO:0000269|PubMed:15961396};
CC KM=0.3 mM for GlcNAc(6) {ECO:0000269|PubMed:15961396};
CC Vmax=24.3 umol/min/mg enzyme with GlcNAc(2) as substrate
CC {ECO:0000269|PubMed:15961396};
CC Vmax=30.6 umol/min/mg enzyme with GlcNAc(3) as substrate
CC {ECO:0000269|PubMed:15961396};
CC Vmax=47.3 umol/min/mg enzyme with GlcNAc(4) as substrate
CC {ECO:0000269|PubMed:15961396};
CC Vmax=15.5 umol/min/mg enzyme with GlcNAc(5) as substrate
CC {ECO:0000269|PubMed:15961396};
CC Vmax=13.4 umol/min/mg enzyme with GlcNAc(6) as substrate
CC {ECO:0000269|PubMed:15961396};
CC pH dependence:
CC Optimum pH is 6.0. {ECO:0000269|PubMed:15961396};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius.
CC {ECO:0000269|PubMed:15961396};
CC -!- PTM: Hydroxylated on Pro-179. Hydroxylation alters the active site and
CC enhances significantly deacetylase activity, probably by creating a
CC more favorable environment for transition-state stabilization. It might
CC be autocatalytic. {ECO:0000269|PubMed:28333455}.
CC -!- SIMILARITY: Belongs to the polysaccharide deacetylase family.
CC {ECO:0000305}.
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DR EMBL; AE016877; AAP08931.1; -; Genomic_DNA.
DR RefSeq; NP_831730.1; NC_004722.1.
DR RefSeq; WP_000291199.1; NZ_CP034551.1.
DR PDB; 4L1G; X-ray; 2.34 A; A/B/C/D=9-275.
DR PDB; 5O6Y; X-ray; 2.50 A; A/B/C/D=61-274.
DR PDBsum; 4L1G; -.
DR PDBsum; 5O6Y; -.
DR AlphaFoldDB; Q81EK9; -.
DR SMR; Q81EK9; -.
DR STRING; 226900.BC_1960; -.
DR BindingDB; Q81EK9; -.
DR ChEMBL; CHEMBL4295615; -.
DR EnsemblBacteria; AAP08931; AAP08931; BC_1960.
DR KEGG; bce:BC1960; -.
DR PATRIC; fig|226900.8.peg.1966; -.
DR HOGENOM; CLU_021264_0_4_9; -.
DR OMA; GMEPLAW; -.
DR BioCyc; MetaCyc:MON-15494; -.
DR BRENDA; 3.5.1.104; 648.
DR SABIO-RK; Q81EK9; -.
DR Proteomes; UP000001417; Chromosome.
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 InterPro; IPR011330; Glyco_hydro/deAcase_b/a-brl.
DR InterPro; IPR002509; NODB_dom.
DR Pfam; PF01522; Polysacc_deac_1; 1.
DR SUPFAM; SSF88713; SSF88713; 1.
DR PROSITE; PS51677; NODB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Hydroxylation; Metal-binding; Reference proteome;
KW Zinc.
FT CHAIN 1..275
FT /note="Peptidoglycan-N-acetylglucosamine deacetylase
FT BC_1960"
FT /id="PRO_0000447692"
FT DOMAIN 81..262
FT /note="NodB homology"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT ACT_SITE 88
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT ACT_SITE 233
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT BINDING 89
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.6"
FT BINDING 139
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.6"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.6"
FT MOD_RES 179
FT /note="2-hydroxyproline; partial"
FT /evidence="ECO:0000269|PubMed:28333455"
FT HELIX 63..69
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 80..90
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 100..105
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 116..121
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 123..131
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 151..169
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:5O6Y"
FT HELIX 185..193
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 213..223
FT /evidence="ECO:0007829|PDB:4L1G"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 241..256
FT /evidence="ECO:0007829|PDB:4L1G"
FT HELIX 264..267
FT /evidence="ECO:0007829|PDB:4L1G"
SQ SEQUENCE 275 AA; 31652 MW; 915046AEE0AC6EBF CRC64;
MYYFYSPEMF APYQWGLERD VSYAYMPYNS FYYGDYINSL PYAYIPQNYE VQMKADDRGS
WTPFSWVEKY AYAFSGPYNK AEVALTFDDG PDLEFTPKIL DKLKQHNVKA TFFLLGENAE
KFPNIVKRIA NEGHVIGNHT YSHPNLAKVN EDEYRNQIIK TEEILNRLAG YAPKFIRPPY
GEILENQLKW ATEQNFMIVQ WSVDTVDWKG VSADTITNNV LGNSFPGSVI LQHSTPGGHL
QGSVDALDKI IPQLKTKGAR FVTLPSMFQT SKERK
