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==Metallo-enzyme from P. marina==
 
<StructureSection load='4mcw' size='340' side='right' caption='[[4mcw]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
==Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre==
<StructureSection load='4mcw' size='340' side='right'caption='[[4mcw]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4mcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Permh Permh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MCW FirstGlance]. <br>
<table><tr><td colspan='2'>[[4mcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Persephonella_marina_EX-H1 Persephonella marina EX-H1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MCW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2.03&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PERMA_0986 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=123214 PERMH])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.1 3.1.4.1] </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=4mcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mcw OCA], [https://pdbe.org/4mcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mcw RCSB], [https://www.ebi.ac.uk/pdbsum/4mcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mcw 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=4mcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mcw RCSB], [http://www.ebi.ac.uk/pdbsum/4mcw PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/C0QQ26_PERMH C0QQ26_PERMH]
Bis-(3',5') cyclic di-guanylate (c-di-GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c-di-GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD-GYP domains. Here, we have determined the structure of an enzymatically active HD-GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c-di-GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c-di-GMP. This structure completes the picture of all domains involved in c-di-GMP metabolism and reveals that the HD-GYP family splits into two distinct subgroups containing bi- and trinuclear metal centres.
 
Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.,Bellini D, Caly DL, McCarthy Y, Bumann M, An SQ, Dow JM, Ryan RP, Walsh MA Mol Microbiol. 2014 Jan;91(1):26-38. doi: 10.1111/mmi.12447. Epub 2013 Nov 24. PMID:24176013<ref>PMID:24176013</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: Permh]]
[[Category: Large Structures]]
[[Category: Phosphodiesterase I]]
[[Category: Persephonella marina EX-H1]]
[[Category: Bellini, D]]
[[Category: Bellini D]]
[[Category: OPPF, Oxford Protein Production Facility]]
[[Category: Walsh MA]]
[[Category: Walsh, M A]]
[[Category: Hydrolase]]
[[Category: Oppf]]
[[Category: Oxford protein production facility]]
[[Category: Structural genomic]]

Latest revision as of 12:25, 1 March 2024

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

4mcw, resolution 2.03Å

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