4wcm: Difference between revisions

Latest revision as of 09:23, 15 November 2023

Crystal Structure of Cell Shape Determinant protein Csd4 Gln46His variant from Helicobacter pylori

Structural highlights

4wcm is a 1 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.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	API, IOD, PO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B5ZAD9_HELPG

Publication Abstract from PubMed

Peptidoglycan (PG) modifying carboxypeptidases (CPs) are important determinants of bacterial cell shape. Here, we report crystal structures of Csd4, a three-domain protein from the human gastric pathogen Helicobacter pylori. The catalytic zinc in Csd4 is coordinated by a rare H+E+Q configuration that is conserved amongst most Csd4 homologs, which form a distinct subfamily of CPs. Substitution of the glutamine to histidine, the residue found in prototypical zinc carboxypeptidases, resulted in decreased enzyme activity and inhibition by phosphate. Expression of the histidine variant at the native locus in a H. pylori csd4 deletion strain did not restore the wild-type helical morphology. Biochemical assays show that Csd4 can cleave a tripeptide PG substrate analog to release m-DAP. Structures of Csd4 with this substrate analog or product bound at the active site reveal determinants of peptidoglycan specificity and the mechanism to cleave an isopeptide bond to release m-DAP. Our data suggest that Csd4 is the archetype of a new CP subfamily with a domain scheme that differs from this large family of peptide cleaving enzymes.

Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4.,Chan AC, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy ME J Biol Chem. 2014 Dec 12. pii: jbc.M114.624734. PMID:25505267^[1]

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

References

↑ Chan AC, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy ME. Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4. J Biol Chem. 2014 Dec 12. pii: jbc.M114.624734. PMID:25505267 doi:https://dx.doi.org/10.1074/jbc.M114.624734

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OCA

[1] Chan AC, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy ME. Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4. J Biol Chem. 2014 Dec 12. pii: jbc.M114.624734. PMID:25505267 doi:https://dx.doi.org/10.1074/jbc.M114.624734

[1]

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Cell Shape Determinant protein Csd4 Gln46His variant from Helicobacter pylori==
-<StructureSection load='4wcm' size='340' side='right' caption='[[4wcm]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='4wcm' size='340' side='right'caption='[[4wcm]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4wcm]] is a 1 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=4WCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WCM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4wcm]] is a 1 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=4WCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WCM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.75&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4wck|4wck]], [[4wcl|4wcl]], [[4wcn|4wcn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HPG27_353 ([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=4wcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcm OCA], [https://pdbe.org/4wcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wcm RCSB], [https://www.ebi.ac.uk/pdbsum/4wcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcm 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=4wcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcm OCA], [http://pdbe.org/4wcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wcm RCSB], [http://www.ebi.ac.uk/pdbsum/4wcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcm ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B5ZAD9_HELPG B5ZAD9_HELPG]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Helpg]]
+[[Category: Helicobacter pylori G27]]
-[[Category: Chan, A C]]
+[[Category: Large Structures]]
-[[Category: Murphy, M E]]
+[[Category: Chan AC]]
-[[Category: Carboxypeptidase]]
+[[Category: Murphy ME]]
-[[Category: Hydrolase]]
-[[Category: M14]]
-[[Category: Mixed alpha beta sandwich]]

4wcm: Difference between revisions

Latest revision as of 09:23, 15 November 2023

Crystal Structure of Cell Shape Determinant protein Csd4 Gln46His variant from Helicobacter pylori

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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