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Peptidoglycan-N-acetylglucosamine deacetylase (Peptidoglycan GlcNAc deacetylase) (EC 3.5.1.104) (Peptidoglycan N-deacetylase) (PG N-deacetylase)

 PGDA_STRR6              Reviewed;         463 AA.
Q8DP63;
13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
07-JUN-2017, entry version 92.
RecName: Full=Peptidoglycan-N-acetylglucosamine deacetylase {ECO:0000303|PubMed:10781617};
Short=Peptidoglycan GlcNAc deacetylase {ECO:0000305};
EC=3.5.1.104 {ECO:0000269|PubMed:10781617, ECO:0000269|PubMed:16221761};
AltName: Full=Peptidoglycan N-deacetylase {ECO:0000303|PubMed:16221761};
Short=PG N-deacetylase {ECO:0000305};
Name=pgdA {ECO:0000303|PubMed:10781617}; OrderedLocusNames=spr1333;
Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
Streptococcus.
NCBI_TaxID=171101;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC BAA-255 / R6;
PubMed=11544234; DOI=10.1128/JB.183.19.5709-5717.2001;
Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E.,
LeBlanc D.J., Lee L.N., Lefkowitz E.J., Lu J., Matsushima P.,
McAhren S.M., McHenney M., McLeaster K., Mundy C.W., Nicas T.I.,
Norris F.H., O'Gara M., Peery R.B., Robertson G.T., Rockey P.,
Sun P.-M., Winkler M.E., Yang Y., Young-Bellido M., Zhao G.,
Zook C.A., Baltz R.H., Jaskunas S.R., Rosteck P.R. Jr., Skatrud P.L.,
Glass J.I.;
"Genome of the bacterium Streptococcus pneumoniae strain R6.";
J. Bacteriol. 183:5709-5717(2001).
[2]
FUNCTION, CATALYTIC ACTIVITY, GENE NAME, AND DISRUPTION PHENOTYPE.
STRAIN=R36A;
PubMed=10781617; DOI=10.1074/jbc.M910189199;
Vollmer W., Tomasz A.;
"The pgdA gene encodes for a peptidoglycan N-acetylglucosamine
deacetylase in Streptococcus pneumoniae.";
J. Biol. Chem. 275:20496-20501(2000).
[3]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=R36A;
PubMed=12438406; DOI=10.1128/IAI.70.12.7176-7178.2002;
Vollmer W., Tomasz A.;
"Peptidoglycan N-acetylglucosamine deacetylase, a putative virulence
factor in Streptococcus pneumoniae.";
Infect. Immun. 70:7176-7178(2002).
[4]
X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 38-463 OF WILD-TYPE AND
MUTANT ASN-275 IN COMPLEX WITH ACETATE PRODUCT AND ZINC, FUNCTION,
CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL
PROPERTIES, REACTION MECHANISM, ACTIVE SITE, AND MUTAGENESIS OF
ASP-275; HIS-326; ARG-364; ASP-391 AND HIS-417.
PubMed=16221761; DOI=10.1073/pnas.0504339102;
Blair D.E., Schuttelkopf A.W., MacRae J.I., van Aalten D.M.;
"Structure and metal-dependent mechanism of peptidoglycan deacetylase,
a streptococcal virulence factor.";
Proc. Natl. Acad. Sci. U.S.A. 102:15429-15434(2005).
-!- FUNCTION: Catalyzes the deacetylation of N-acetylglucosamine
(GlcNAc) residues in peptidoglycan, a modification that confers
host lysozyme resistance and contributes to pneumococcal
virulence. {ECO:0000269|PubMed:10781617,
ECO:0000269|PubMed:12438406, ECO:0000269|PubMed:16221761}.
-!- CATALYTIC ACTIVITY: Peptidoglycan-N-acetyl-D-glucosamine + H(2)O =
peptidoglycan-D-glucosamine + acetate.
{ECO:0000269|PubMed:10781617, ECO:0000269|PubMed:16221761}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:16221761};
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Evidence={ECO:0000269|PubMed:16221761};
Note=Zn(2+). Although displays higher activity with Co(2+) than
with Zn(2+) in vitro, bioavailability may well limit this enzyme
to be zinc-dependent. {ECO:0000269|PubMed:16221761};
-!- ENZYME REGULATION: Enzymatic activity is inhibited by EDTA in
vitro. {ECO:0000269|PubMed:16221761}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=3.8 mM for GlcNAc3 {ECO:0000269|PubMed:16221761};
Note=kcat is 0.55 sec(-1) with GlcNAc3 as substrate.
{ECO:0000269|PubMed:16221761};
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass
membrane protein {ECO:0000305}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene produce fully N-
acetylated glycan, become hypersensitive to exogenous lysozyme in
the stationary phase of growth, and show reduced virulence in the
intraperitoneal mouse model. {ECO:0000269|PubMed:10781617,
ECO:0000269|PubMed:12438406}.
-----------------------------------------------------------------------
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EMBL; AE007317; AAL00137.1; -; Genomic_DNA.
PIR; D98038; D98038.
RefSeq; NP_358926.1; NC_003098.1.
RefSeq; WP_001854799.1; NC_003098.1.
PDB; 2C1G; X-ray; 1.75 A; A=38-463.
PDB; 2C1I; X-ray; 1.35 A; A=38-463.
PDBsum; 2C1G; -.
PDBsum; 2C1I; -.
ProteinModelPortal; Q8DP63; -.
SMR; Q8DP63; -.
STRING; 171101.spr1333; -.
BindingDB; Q8DP63; -.
EnsemblBacteria; AAL00137; AAL00137; spr1333.
GeneID; 934547; -.
KEGG; spr:spr1333; -.
PATRIC; fig|171101.6.peg.1445; -.
eggNOG; ENOG4108ZJ4; Bacteria.
eggNOG; COG0726; LUCA.
HOGENOM; HOG000235351; -.
OMA; FFMMGSK; -.
BRENDA; 3.5.1.104; 1960.
EvolutionaryTrace; Q8DP63; -.
Proteomes; UP000000586; Chromosome.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0016020; C:membrane; IBA:GO_Central.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
GO; GO:0009405; P:pathogenesis; IEA:UniProtKB-KW.
InterPro; IPR011330; Glyco_hydro/deAcase_b/a-brl.
InterPro; IPR002509; NODB_dom.
InterPro; IPR017219; Peptidoglycan_deacetylase.
Pfam; PF01522; Polysacc_deac_1; 1.
PIRSF; PIRSF037479; PG_GlcNAc_deacetylase; 1.
SUPFAM; SSF88713; SSF88713; 1.
PROSITE; PS51677; NODB; 1.
1: Evidence at protein level;
3D-structure; Carbohydrate metabolism; Cell membrane; Cobalt;
Complete proteome; Hydrolase; Membrane; Metal-binding;
Reference proteome; Transmembrane; Transmembrane helix; Virulence;
Zinc.
CHAIN 1 463 Peptidoglycan-N-acetylglucosamine
deacetylase.
/FTId=PRO_0000424440.
TRANSMEM 18 38 Helical. {ECO:0000255}.
DOMAIN 268 442 NodB homology. {ECO:0000255|PROSITE-
ProRule:PRU01014}.
ACT_SITE 275 275 Proton acceptor.
{ECO:0000269|PubMed:16221761}.
ACT_SITE 417 417 Proton donor.
{ECO:0000269|PubMed:16221761}.
METAL 276 276 Zinc. {ECO:0000269|PubMed:16221761}.
METAL 326 326 Zinc; via tele nitrogen.
{ECO:0000269|PubMed:16221761}.
METAL 330 330 Zinc; via tele nitrogen.
{ECO:0000269|PubMed:16221761}.
BINDING 367 367 Substrate; via amide nitrogen.
{ECO:0000269|PubMed:16221761}.
SITE 391 391 Raises pKa of active site His.
{ECO:0000269|PubMed:16221761}.
MUTAGEN 275 275 D->N: Loss of activity.
{ECO:0000269|PubMed:16221761}.
MUTAGEN 326 326 H->A: Loss of activity.
{ECO:0000269|PubMed:16221761}.
MUTAGEN 364 364 R->S: Loss of activity.
{ECO:0000269|PubMed:16221761}.
MUTAGEN 391 391 D->N: Loss of activity.
{ECO:0000269|PubMed:16221761}.
MUTAGEN 417 417 H->S: Loss of activity.
{ECO:0000269|PubMed:16221761}.
HELIX 47 61 {ECO:0000244|PDB:2C1I}.
STRAND 65 72 {ECO:0000244|PDB:2C1I}.
STRAND 75 84 {ECO:0000244|PDB:2C1I}.
HELIX 90 102 {ECO:0000244|PDB:2C1I}.
STRAND 110 119 {ECO:0000244|PDB:2C1I}.
STRAND 125 135 {ECO:0000244|PDB:2C1I}.
STRAND 138 141 {ECO:0000244|PDB:2C1G}.
STRAND 144 156 {ECO:0000244|PDB:2C1I}.
HELIX 164 167 {ECO:0000244|PDB:2C1I}.
HELIX 171 184 {ECO:0000244|PDB:2C1I}.
HELIX 208 210 {ECO:0000244|PDB:2C1I}.
STRAND 213 216 {ECO:0000244|PDB:2C1I}.
STRAND 219 222 {ECO:0000244|PDB:2C1I}.
STRAND 234 237 {ECO:0000244|PDB:2C1I}.
HELIX 238 244 {ECO:0000244|PDB:2C1I}.
HELIX 247 249 {ECO:0000244|PDB:2C1I}.
HELIX 252 265 {ECO:0000244|PDB:2C1I}.
STRAND 269 276 {ECO:0000244|PDB:2C1I}.
TURN 280 282 {ECO:0000244|PDB:2C1I}.
HELIX 283 292 {ECO:0000244|PDB:2C1I}.
STRAND 298 301 {ECO:0000244|PDB:2C1I}.
HELIX 303 305 {ECO:0000244|PDB:2C1I}.
TURN 306 308 {ECO:0000244|PDB:2C1I}.
HELIX 310 318 {ECO:0000244|PDB:2C1I}.
STRAND 322 325 {ECO:0000244|PDB:2C1I}.
HELIX 333 335 {ECO:0000244|PDB:2C1I}.
HELIX 338 356 {ECO:0000244|PDB:2C1I}.
HELIX 366 368 {ECO:0000244|PDB:2C1I}.
HELIX 372 376 {ECO:0000244|PDB:2C1I}.
STRAND 381 383 {ECO:0000244|PDB:2C1I}.
STRAND 386 388 {ECO:0000244|PDB:2C1I}.
HELIX 391 394 {ECO:0000244|PDB:2C1I}.
HELIX 397 407 {ECO:0000244|PDB:2C1I}.
STRAND 412 417 {ECO:0000244|PDB:2C1I}.
HELIX 421 436 {ECO:0000244|PDB:2C1I}.
HELIX 444 448 {ECO:0000244|PDB:2C1I}.
HELIX 449 451 {ECO:0000244|PDB:2C1I}.
STRAND 457 461 {ECO:0000244|PDB:2C1I}.
SEQUENCE 463 AA; 52675 MW; 12E1935E66521EDE CRC64;
MNKSRLGRGR HGKTRHVLLA LIGILAISIC LLGGFIAFKI YQQKSFEQKI ESLKKEKDDQ
LSEGNQKEHF RQGQAEVIAY YPLQGEKVIS SVRELINQDV KDKLESKDNL VFYYTEQEES
GLKGVVNRNV TKQIYDLVAF KIEETEKTSL GKVHLTEDGQ PFTLDQLFSD ASKAKEQLIK
ELTSFIEDKK IEQDQSEQIV KNFSDQDLSA WNFDYKDSQI ILYPSPVVEN LEEIALPVSA
FFDVIQSSYL LEKDAALYQS YFDKKHQKVV ALTFDDGPNP ATTPQVLETL AKYDIKATFF
VLGKNVSGNE DLVKRIKSEG HVVGNHSWSH PILSQLSLDE AKKQITDTED VLTKVLGSSS
KLMRPPYGAI TDDIRNSLDL SFIMWDVDSL DWKSKNEASI LTEIQHQVAN GSIVLMHDIH
SPTVNALPRV IEYLKNQGYT FVTIPEMLNT RLKAHELYYS RDE


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