4wcl: Difference between revisions

Revision as of 07:02, 7 April 2023

Crystal Structure of product bound Cell Shape Determinant protein Csd4 from Helicobacter pylori

Structural highlights

4wcl 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.
Ligands:	API, IOD, NA, 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 product bound Cell Shape Determinant protein Csd4 from Helicobacter pylori==
-<StructureSection load='4wcl' size='340' side='right' caption='[[4wcl]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='4wcl' size='340' side='right'caption='[[4wcl]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4wcl]] 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=4WCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WCL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4wcl]] 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=4WCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WCL 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=NA:SODIUM+ION'>NA</scene>, <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=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4wck|4wck]], [[4wcm|4wcm]], [[4wcn|4wcn]]</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=4wcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcl OCA], [https://pdbe.org/4wcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wcl RCSB], [https://www.ebi.ac.uk/pdbsum/4wcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcl ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4wcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcl OCA], [http://pdbe.org/4wcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wcl RCSB], [http://www.ebi.ac.uk/pdbsum/4wcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcl 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 22: @@
 __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]]

4wcl: Difference between revisions

Revision as of 07:02, 7 April 2023

Crystal Structure of product bound Cell Shape Determinant protein Csd4 from Helicobacter pylori

Structural highlights

Function

Publication Abstract from PubMed

References

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