5jsp

From Proteopedia

(Difference between revisions)

Current revision

New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ

Structural highlights

5jsp is a 2 chain structure with sequence from Ruegeria lacuscaerulensis ITI-1157. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

Publication Abstract from PubMed

The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates approximately 300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP beta-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses approximately 0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.

New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ.,Brummett AE, Dey M Biochemistry. 2016 Nov 8;55(44):6162-6174. Epub 2016 Oct 28. PMID:27755868^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry. 2016 Nov 8;55(44):6162-6174. Epub 2016 Oct 28. PMID:27755868 doi:http://dx.doi.org/10.1021/acs.biochem.6b00585

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jsp"

Categories: Large Structures | Ruegeria lacuscaerulensis ITI-1157 | Brummett AE | Dey M

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5jsp is ON HOLD  until Paper Publication
+==New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ==
+<StructureSection load='5jsp' size='340' side='right'caption='[[5jsp]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5jsp]] 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=5JSP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JSP 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DQY:3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC+ACID'>DQY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5jsp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsp OCA], [https://pdbe.org/5jsp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jsp RCSB], [https://www.ebi.ac.uk/pdbsum/5jsp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsp 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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates approximately 300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP beta-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses approximately 0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.
-Authors:
+New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ.,Brummett AE, Dey M Biochemistry. 2016 Nov 8;55(44):6162-6174. Epub 2016 Oct 28. PMID:27755868<ref>PMID:27755868</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5jsp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Ruegeria lacuscaerulensis ITI-1157]]
+[[Category: Brummett AE]]
+[[Category: Dey M]]

5jsp

From Proteopedia

Current revision

New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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