PGDA2_BACCR
ID PGDA2_BACCR Reviewed; 273 AA.
AC Q81EJ6;
DT 31-JUL-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Peptidoglycan-N-acetylglucosamine deacetylase BC_1974 {ECO:0000303|PubMed:29257674};
DE Short=Peptidoglycan GlcNAc deacetylase {ECO:0000305};
DE EC=3.5.1.104 {ECO:0000269|PubMed:29983281};
GN OrderedLocusNames=BC_1974 {ECO:0000312|EMBL:AAP08945.1};
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, COFACTOR, ACTIVITY REGULATION, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
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 [3] {ECO:0007744|PDB:5N1J, ECO:0007744|PDB:5N1P, ECO:0007744|PDB:5NC6, ECO:0007744|PDB:5NC9, ECO:0007744|PDB:5NCD, ECO:0007744|PDB:5NEK, ECO:0007744|PDB:5NEL}
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEXES WITH ZINC AND ZINC
RP METALLOENZYME INHIBITORS, COFACTOR, AND ACTIVE SITE.
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=29257674; DOI=10.1021/acs.biochem.7b00919;
RA Giastas P., Andreou A., Papakyriakou A., Koutsioulis D., Balomenou S.,
RA Tzartos S.J., Bouriotis V., Eliopoulos E.E.;
RT "Structures of the peptidoglycan N-acetylglucosamine deacetylase Bc1974 and
RT its complexes with zinc metalloenzyme inhibitors.";
RL Biochemistry 57:753-763(2018).
CC -!- FUNCTION: Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc)
CC residues in peptidoglycan. {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:29983281};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:29257674, ECO:0000269|PubMed:29983281};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:29983281};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:29983281};
CC -!- ACTIVITY REGULATION: Inhibited by the hydroxamate N-hydroxy-4-
CC (naphthalene-1-yl)benzamide (NHNB). {ECO:0000269|PubMed:29983281}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.8 mM for GlcNAc(5) {ECO:0000269|PubMed:29983281};
CC Note=kcat is 3000 sec(-1) with GlcNAc(5) as substrate.
CC {ECO:0000269|PubMed:29983281};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the polysaccharide deacetylase family.
CC {ECO:0000305}.
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DR EMBL; AE016877; AAP08945.1; -; Genomic_DNA.
DR RefSeq; NP_831744.1; NC_004722.1.
DR RefSeq; WP_000409484.1; NZ_CP034551.1.
DR PDB; 5N1J; X-ray; 1.80 A; A/B/C/D=68-273.
DR PDB; 5N1P; X-ray; 1.45 A; A/B/C/D=68-273.
DR PDB; 5NC6; X-ray; 2.80 A; A=69-273, B/C/D=1-273.
DR PDB; 5NC9; X-ray; 2.44 A; A/B/C/D=27-273.
DR PDB; 5NCD; X-ray; 2.45 A; A/B/C/D=27-273.
DR PDB; 5NEK; X-ray; 3.06 A; A/B/C/D=27-273.
DR PDB; 5NEL; X-ray; 2.73 A; A/B/C/D=27-273.
DR PDBsum; 5N1J; -.
DR PDBsum; 5N1P; -.
DR PDBsum; 5NC6; -.
DR PDBsum; 5NC9; -.
DR PDBsum; 5NCD; -.
DR PDBsum; 5NEK; -.
DR PDBsum; 5NEL; -.
DR AlphaFoldDB; Q81EJ6; -.
DR SMR; Q81EJ6; -.
DR STRING; 226900.BC_1974; -.
DR BindingDB; Q81EJ6; -.
DR ChEMBL; CHEMBL4295614; -.
DR EnsemblBacteria; AAP08945; AAP08945; BC_1974.
DR GeneID; 67506596; -.
DR KEGG; bce:BC1974; -.
DR PATRIC; fig|226900.8.peg.1980; -.
DR HOGENOM; CLU_021264_6_3_9; -.
DR OMA; AYHEENH; -.
DR BRENDA; 3.5.1.104; 648.
DR SABIO-RK; Q81EJ6; -.
DR Proteomes; UP000001417; 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 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; Cell membrane; Cobalt; Hydrolase; Membrane; Metal-binding;
KW Nickel; Reference proteome; Transmembrane; Transmembrane helix; Zinc.
FT CHAIN 1..273
FT /note="Peptidoglycan-N-acetylglucosamine deacetylase
FT BC_1974"
FT /id="PRO_0000447693"
FT TRANSMEM 10..30
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 69..255
FT /note="NodB homology"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01014"
FT ACT_SITE 76
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:29257674"
FT ACT_SITE 230
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:29257674"
FT BINDING 77
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29257674"
FT BINDING 126
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29257674"
FT BINDING 130
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29257674"
FT STRAND 69..78
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 83..92
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 103..108
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:5N1P"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:5NCD"
FT HELIX 141..156
FT /evidence="ECO:0007829|PDB:5N1P"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 175..183
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 205..219
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 222..230
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 234..249
FT /evidence="ECO:0007829|PDB:5N1P"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:5N1P"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:5N1P"
SQ SEQUENCE 273 AA; 30677 MW; 5A5E179260727FAB CRC64;
MEKALKIKQI VVVLIAIAAV AIGYYMFQSI TSPAKAVAKQ ENVVQLASEQ PKVEMNKTAP
SRFNGKERKV AYLTFDDGPG KYTAELLNTL KQHDAKATFF LIGANVKEFP DLVKRENAEG
HYVGMHSMTH NFAKLYKNGE YVNEMKEDQG LIANIIGKSP KLTRPPYGSM PGLNEGLRNK
VVEGGFKVWD WTIDSLDWRY NKMPVDAAAA QIAQNVLTNA TKPQEVILMH DIHPQSVAAV
PAILKGLKEK GYEFEAYHEE SHFPVNFWHD NRM
