View source for 4b28


==Crystal structure of DMSP lyase RdDddP from Roseobacter denitrificans==
<StructureSection load='4b28' size='340' side='right'caption='[[4b28]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4b28]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseobacter_denitrificans_OCh_114 Roseobacter denitrificans OCh 114]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B28 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=4b28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b28 OCA], [https://pdbe.org/4b28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b28 RCSB], [https://www.ebi.ac.uk/pdbsum/4b28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b28 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DDDP_ROSDO DDDP_ROSDO] Able to cleave dimethylsulfonioproprionate (DMSP), releasing dimethyl sulfide (DMS). DMS is the principal form by which sulfur is transported from oceans to the atmosphere. The real activity of the protein is however subject to debate and it is unclear whether it constitutes a real dimethylsulfonioproprionate lyase in vivo: the low activity with DMSP as substrate suggests that DMSP is not its native substrate.[UniProtKB:A3SK19]
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== Publication Abstract from PubMed ==
Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 A resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 A apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.

The Structure of RdDddP from Roseobacter denitrificans Reveals That DMSP Lyases in the DddP-Family Are Metalloenzymes.,Hehemann JH, Law A, Redecke L, Boraston AB PLoS One. 2014 Jul 23;9(7):e103128. doi: 10.1371/journal.pone.0103128., eCollection 2014. PMID:25054772<ref>PMID:25054772</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 4b28" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Roseobacter denitrificans OCh 114]]
[[Category: Boraston AB]]
[[Category: Hehemann JH]]
[[Category: Law A]]
[[Category: Redecke L]]