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| | <StructureSection load='2c1i' size='340' side='right'caption='[[2c1i]], [[Resolution|resolution]] 1.35Å' scene=''> | | <StructureSection load='2c1i' size='340' side='right'caption='[[2c1i]], [[Resolution|resolution]] 1.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2c1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C1I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2c1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C1I FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2c1g|2c1g]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylglucosamine_deacetylase N-acetylglucosamine deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.33 3.5.1.33] </span></td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1i OCA], [https://pdbe.org/2c1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c1i RCSB], [https://www.ebi.ac.uk/pdbsum/2c1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c1i ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1i OCA], [https://pdbe.org/2c1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c1i RCSB], [https://www.ebi.ac.uk/pdbsum/2c1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c1i ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PGDA_STRR6 PGDA_STRR6] Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan, a modification that confers host lysozyme resistance and contributes to pneumococcal virulence.<ref>PMID:10781617</ref> <ref>PMID:12438406</ref> <ref>PMID:16221761</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: N-acetylglucosamine deacetylase]] | + | [[Category: Streptococcus pneumoniae R6]] |
| - | [[Category: Strr6]]
| + | [[Category: Blair DE]] |
| - | [[Category: Aalten, D M.F van]]
| + | [[Category: MacRae JI]] |
| - | [[Category: Blair, D E]] | + | [[Category: Schuttelkopf AW]] |
| - | [[Category: MacRae, J I]] | + | [[Category: Van Aalten DMF]] |
| - | [[Category: Schuttelkopf, A W]] | + | |
| - | [[Category: Carbohydrate esterase]] | + | |
| - | [[Category: Ce-4]]
| + | |
| - | [[Category: D275n mutant]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Peptidoglycan deacetylase]]
| + | |
| Structural highlights
Function
PGDA_STRR6 Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan, a modification that confers host lysozyme resistance and contributes to pneumococcal virulence.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA) protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. Deletion of the pgda gene has been shown to result in hypersensitivity to lysozyme and reduction of infectivity in a mouse model. SpPgdA is a member of the family 4 carbohydrate esterases, for which little structural information exists, and no catalytic mechanism has yet been defined. Here we describe the native crystal structure and product complexes of SpPgdA biochemical characterization and mutagenesis. The structural data show that SpPgdA is an elongated three-domain protein in the crystal. The structure, in combination with mutagenesis, shows that SpPgdA is a metalloenzyme using a His-His-Asp zinc-binding triad with a nearby aspartic acid and histidine acting as the catalytic base and acid, respectively, somewhat similar to other zinc deacetylases such as LpxC. The enzyme is able to accept GlcNAc(3) as a substrate (K(m) = 3.8 mM, k(cat) = 0.55 s(-1)), with the N-acetyl of the middle sugar being removed by the enzyme. The data described here show that SpPgdA and the other family 4 carbohydrate esterases are metalloenzymes and present a step toward identification of mechanism-based inhibitors for this important class of enzymes.
Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor.,Blair DE, Schuttelkopf AW, MacRae JI, van Aalten DM Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15429-34. Epub 2005 Oct 12. PMID:16221761[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Vollmer W, Tomasz A. The pgdA gene encodes for a peptidoglycan N-acetylglucosamine deacetylase in Streptococcus pneumoniae. J Biol Chem. 2000 Jul 7;275(27):20496-501. PMID:10781617 doi:10.1074/jbc.M910189199
- ↑ Vollmer W, Tomasz A. Peptidoglycan N-acetylglucosamine deacetylase, a putative virulence factor in Streptococcus pneumoniae. Infect Immun. 2002 Dec;70(12):7176-8. PMID:12438406 doi:10.1128/IAI.70.12.7176-7178.2002
- ↑ Blair DE, Schuttelkopf AW, MacRae JI, van Aalten DM. Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15429-34. Epub 2005 Oct 12. PMID:16221761
- ↑ Blair DE, Schuttelkopf AW, MacRae JI, van Aalten DM. Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15429-34. Epub 2005 Oct 12. PMID:16221761
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