5xsi: Difference between revisions

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<StructureSection load='5xsi' size='340' side='right'caption='[[5xsi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='5xsi' size='340' side='right'caption='[[5xsi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XSI FirstGlance]. <br>
<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XSI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.2&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [http://pdbe.org/5xsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [http://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [https://pdbe.org/5xsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [https://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A0U1MUE2_STAAU A0A0U1MUE2_STAAU]
The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.
 
Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.,Wang F, He Q, Su K, Wei T, Xu S, Gu L Biochem J. 2018 Jan 5;475(1):191-205. doi: 10.1042/BCJ20170739. PMID:29203646<ref>PMID:29203646</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xsi" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gu, L]]
[[Category: Staphylococcus aureus]]
[[Category: Wang, F]]
[[Category: Gu L]]
[[Category: Hydrolase]]
[[Category: Wang F]]
[[Category: Phosphodiesterase]]

Latest revision as of 10:20, 27 March 2024

The catalytic domain of GdpP

5xsi, resolution 2.20Å

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