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| | ==Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ== | | ==Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ== |
| - | <StructureSection load='4la2' size='340' side='right' caption='[[4la2]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='4la2' size='340' side='right'caption='[[4la2]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4la2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Silicibacter_lacuscaerulensis_dsm_11314 Silicibacter lacuscaerulensis dsm 11314]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LA2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LA2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4la2]] 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=4LA2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LA2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4la3|4la3]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SL1157_0332 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644107 Silicibacter lacuscaerulensis DSM 11314])</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=4la2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4la2 OCA], [https://pdbe.org/4la2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4la2 RCSB], [https://www.ebi.ac.uk/pdbsum/4la2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4la2 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=4la2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4la2 OCA], [http://pdbe.org/4la2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4la2 RCSB], [http://www.ebi.ac.uk/pdbsum/4la2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4la2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [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> |
| - | 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.
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| - | 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>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div> | + | |
| - | <div class="pdbe-citations 4la2" style="background-color:#fffaf0;"></div> | + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Silicibacter lacuscaerulensis dsm 11314]] | + | [[Category: Large Structures]] |
| - | [[Category: Li, C]] | + | [[Category: Ruegeria lacuscaerulensis ITI-1157]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Li C]] |
| - | [[Category: Cupin motif]] | + | [[Category: Zhang Y]] |
| - | [[Category: Dmsp lyase]]
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| - | [[Category: Lyase]]
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| Structural highlights
Function
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).[1] [2] [3]
References
- ↑ 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. Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide. 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 doi:http://dx.doi.org/10.1073/pnas.1312354111
- ↑ Alcolombri U, Elias M, Vardi A, Tawfik DS. Ambiguous evidence for assigning DddQ as a dimethylsulfoniopropionate lyase and oceanic dimethylsulfide producer. Proc Natl Acad Sci U S A. 2014 May 20;111(20):E2078-9. doi:, 10.1073/pnas.1401685111. Epub 2014 Apr 23. PMID:24760823 doi:http://dx.doi.org/10.1073/pnas.1401685111
- ↑ Li CY, Chen XL, Xie BB, Su HN, Qin QL, Zhang YZ. Reply to Tawfik et al.: DddQ is a dimethylsulfoniopropionate lyase involved in dimethylsulfoniopropionate catabolism in marine bacterial cells. Proc Natl Acad Sci U S A. 2014 May 20;111(20):E2080. PMID:24967457
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