View source for 4la3


==Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ Y131A in complex with DMSP==
<StructureSection load='4la3' size='340' side='right'caption='[[4la3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4la3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_lacuscaerulensis_ITI-1157 Ruegeria lacuscaerulensis ITI-1157]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LA3 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]] 2.701&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</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'>[https://proteopedia.org/fgij/fg.htm?mol=4la3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4la3 OCA], [https://pdbe.org/4la3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4la3 RCSB], [https://www.ebi.ac.uk/pdbsum/4la3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4la3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DDDQ_RUELI DDDQ_RUELI] Able to cleave dimethlysulfonioproprionate (DMSP) in vitro, releasing dimethyl sulfide (DMS). DMS is the principal form by which sulfur is transported from oceans to the atmosphere (PubMed:24395783, PubMed:24967457). The real activity of the protein is however subject to debate and it is unclear whether it constitutes a real dimethlysulfonioproprionate lyase in vivo: the very low activity with DMSP as substrate suggests that DMSP is not its native substrate (PubMed:24760823).<ref>PMID:24395783</ref> <ref>PMID:24760823</ref> <ref>PMID:24967457</ref> 
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== Publication Abstract from PubMed ==
The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a beta-barrel fold structure and contains a Zn(2+) ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the beta-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.

Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide.,Li CY, Wei TD, Zhang SH, Chen XL, Gao X, Wang P, Xie BB, Su HN, Qin QL, Zhang XY, Yu J, Zhang HH, Zhou BC, Yang GP, Zhang YZ Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):1026-31. doi:, 10.1073/pnas.1312354111. Epub 2014 Jan 6. PMID:24395783<ref>PMID:24395783</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 4la3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Ruegeria lacuscaerulensis ITI-1157]]
[[Category: Li C]]
[[Category: Zhang Y]]