4ly4

From Proteopedia

(Difference between revisions)

Revision as of 10:39, 21 December 2022

Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori

Structural highlights

4ly4 is a 4 chain structure with sequence from Helicobacter pylori G27. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGDAE_HELPG Catalyzes the N-deacetylation of peptidoglycan (PG), an important mechanism that appears to confer lysozyme resistance and to mitigate host immune detection; this likely contributes to pathogen persistence in the host. The exact nature of the residue in PG that is deacetylated has not been determined. Is also able to catalyze the deacetylation of acetylated xylan, and, to a lesser extent, that of chitin and chitosan. Therefore, this enzyme might play a role during infection, considering that xylan-containing carbohydrate structures are among those commonly consumed by humans (By similarity). In vitro, does not show activity on N-acetylglucosamine (GlcNAc), chitotriose (GlcNAc3), some N-acetyl-dipeptides and allantoinase.^[1]

Publication Abstract from PubMed

Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. In a recent study, we determined the crystallographic structure of the enzyme, which is a homo-tetramer (Shaik et al., PloS One 2011;6:e19207). The metal-binding site, which is essential for the enzyme's catalytic activity, is visible within the structure, but we were unable to identify the nature of the metal itself. In this study, we have obtained a higher-resolution crystal structure of the enzyme, which shows that the ion bound is, in fact, zinc. Analysis of the structure of the four sites, one per monomer, and quantum chemical calculations of models of the site in the presence of different divalent metal ions show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur. Proteins 2014. (c) 2013 Wiley Periodicals, Inc.

Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.,Munan Shaik M, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G Proteins. 2013 Dec 17. doi: 10.1002/prot.24497. PMID:24346839^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shaik MM, Cendron L, Percudani R, Zanotti G. The Structure of Helicobacter pylori HP0310 Reveals an Atypical Peptidoglycan Deacetylase. PLoS One. 2011 Apr 29;6(4):e19207. PMID:21559431 doi:10.1371/journal.pone.0019207
↑ Munan Shaik M, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G. Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations. Proteins. 2013 Dec 17. doi: 10.1002/prot.24497. PMID:24346839 doi:http://dx.doi.org/10.1002/prot.24497

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ly4"

Categories: Helicobacter pylori G27 | Large Structures | Shaik MM | Zanotti G

@@ Line 1: / Line 1: @@
 ==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==
-<StructureSection load='4ly4' size='340' side='right' caption='[[4ly4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4ly4' size='340' side='right'caption='[[4ly4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_G27 Helicobacter pylori G27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HP0310, HPG27_289 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [https://pdbe.org/4ly4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [http://pdbe.org/4ly4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [http://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGDAE_HELPG PGDAE_HELPG] Catalyzes the N-deacetylation of peptidoglycan (PG), an important mechanism that appears to confer lysozyme resistance and to mitigate host immune detection; this likely contributes to pathogen persistence in the host. The exact nature of the residue in PG that is deacetylated has not been determined. Is also able to catalyze the deacetylation of acetylated xylan, and, to a lesser extent, that of chitin and chitosan. Therefore, this enzyme might play a role during infection, considering that xylan-containing carbohydrate structures are among those commonly consumed by humans (By similarity). In vitro, does not show activity on N-acetylglucosamine (GlcNAc), chitotriose (GlcNAc3), some N-acetyl-dipeptides and allantoinase.<ref>PMID:21559431</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Helpg]]
+[[Category: Helicobacter pylori G27]]
-[[Category: Shaik, M M]]
+[[Category: Large Structures]]
-[[Category: Zanotti, G]]
+[[Category: Shaik MM]]
-[[Category: Deacetylase]]
+[[Category: Zanotti G]]
-[[Category: Hydrolase]]
-[[Category: Metallo enzyme]]
-[[Category: Peptidoglycan]]
-[[Category: Peptidoglycan deacetylase]]
-[[Category: Tim barrel]]

4ly4

From Proteopedia

Revision as of 10:39, 21 December 2022

Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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