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4mcw

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

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Retrieved from "http://52.214.119.220/wiki/index.php/4mcw"

Categories: Large Structures | Persephonella marina EX-H1 | Bellini D | Walsh MA

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 <StructureSection load='4mcw' size='340' side='right'caption='[[4mcw]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4mcw]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/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" 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>
+</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 ([https://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'>[https://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [https://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>
 </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>
-<div class="pdbe-citations 4mcw" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Permh]]
+[[Category: Persephonella marina EX-H1]]
-[[Category: Phosphodiesterase I]]
+[[Category: Bellini D]]
-[[Category: Bellini, D]]
+[[Category: Walsh MA]]
-[[Category: OPPF, Oxford Protein Production Facility]]
-[[Category: Walsh, M A]]
-[[Category: Hydrolase]]
-[[Category: Oppf]]
-[[Category: Oxford protein production facility]]
-[[Category: Structural genomic]]

4mcw

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

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