This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4rnz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:54, 1 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Structure of Helicobacter pylori Csd3 from the hexagonal crystal==
==Structure of Helicobacter pylori Csd3 from the hexagonal crystal==
-
<StructureSection load='4rnz' size='340' side='right' caption='[[4rnz]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
+
<StructureSection load='4rnz' size='340' side='right'caption='[[4rnz]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4rnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RNZ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4rnz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RNZ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.98&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rny|4rny]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4rnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rnz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rnz RCSB], [http://www.ebi.ac.uk/pdbsum/4rnz PDBsum]</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=4rnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rnz OCA], [https://pdbe.org/4rnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rnz RCSB], [https://www.ebi.ac.uk/pdbsum/4rnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rnz ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/O25247_HELPY O25247_HELPY]
-
Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its D,D-endopeptidase activity cleaves the D-Ala(4)-mDAP(3) peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a D,D-carboxypeptidase that cleaves off the terminal D-Ala(5) from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn(2+) ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.
+
-
 
+
-
Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase.,An DR, Kim HS, Kim J, Im HN, Yoon HJ, Yoon JY, Jang JY, Hesek D, Lee M, Mobashery S, Kim SJ, Lee BI, Suh SW Acta Crystallogr D Biol Crystallogr. 2015 Mar 1;71(Pt 3):675-86. doi:, 10.1107/S1399004715000152. Epub 2015 Feb 26. PMID:25760614<ref>PMID:25760614</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: An, D R]]
+
[[Category: Helicobacter pylori 26695]]
-
[[Category: Hesek, D]]
+
[[Category: Large Structures]]
-
[[Category: Im, H N]]
+
[[Category: An DR]]
-
[[Category: Jang, J Y]]
+
[[Category: Hesek D]]
-
[[Category: Kim, H S]]
+
[[Category: Im HN]]
-
[[Category: Kim, J]]
+
[[Category: Jang JY]]
-
[[Category: Kim, S J]]
+
[[Category: Kim HS]]
-
[[Category: Lee, B I]]
+
[[Category: Kim J]]
-
[[Category: Lee, M]]
+
[[Category: Kim S-J]]
-
[[Category: Mobashery, S]]
+
[[Category: Lee BI]]
-
[[Category: Suh, S W]]
+
[[Category: Lee M]]
-
[[Category: Yoon, H J]]
+
[[Category: Mobashery S]]
-
[[Category: Yoon, J Y]]
+
[[Category: Suh SW]]
-
[[Category: Hydrolase]]
+
[[Category: Yoon HJ]]
-
[[Category: M23b metallopeptidase]]
+
[[Category: Yoon JY]]
-
[[Category: Metallopeptidase]]
+
-
[[Category: Peptidoglycan]]
+

Current revision

Structure of Helicobacter pylori Csd3 from the hexagonal crystal

PDB ID 4rnz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rnz"
Personal tools