4izb: Difference between revisions
New page: '''Unreleased structure''' The entry 4izb is ON HOLD Authors: Tan, D., Tong, L. Description: Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and ... |
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The | ==Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA== | ||
<StructureSection load='4izb' size='340' side='right'caption='[[4izb]], [[Resolution|resolution]] 1.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4izb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_pomeroyi_DSS-3 Ruegeria pomeroyi DSS-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IZB 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]] 1.504Å</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=4izb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4izb OCA], [https://pdbe.org/4izb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4izb RCSB], [https://www.ebi.ac.uk/pdbsum/4izb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4izb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DMDD_RUEPO DMDD_RUEPO] Involved in the assimilation of dimethylsulphoniopropionate (DMSP), an important compound in the fixation of carbon in marine phytoplankton, by catalyzing both the hydration and the hydrolysis of 3-(methylthio)acryloyl-CoA (MTA-CoA) to acetaldehyde, CO2, MeSH, and CoA (PubMed:21562561, PubMed:23704947).<ref>PMID:21562561</ref> <ref>PMID:23704947</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Dimethyl-sulphoniopropionate (DMSP) is produced in abundance by marine phytoplankton, and the catabolism of this compound is an important source of carbon and reduced sulfur for marine bacteria and other organisms. The enzyme DmdD catalyzes the last step in the methanethiol (MeSH) pathway of DMSP catabolism. DmdD is a member of the crotonase superfamily of enzymes, and it catalyzes both the hydration and the hydrolysis of methylthioacryloyl-CoA (MTA-CoA), converting it to acetaldehyde, CO2, MeSH, and CoA. We report here the crystal structure of Ruegeria pomeroyi DmdD free enzyme at 1.5 A resolution and the structures of the E121A mutant in complex with MTA-CoA and 3-methylmercaptopropionate-CoA (MMPA-CoA) at 1.8 A resolution. DmdD is a hexamer, composed of a dimer of trimers where the three monomers of each trimer are related by a crystallographic 3-fold axis. The overall structure of this hexamer is similar to those of canonical crotonases. However, the C-terminal loops of DmdD in one of the trimers assume a different conformation and contribute to CoA binding in the active site of a neighboring monomer of the trimer, while these loops in the second trimer are disordered. MTA-CoA is bound deep in the active site in the first trimer, but shows a 1.5 A shift in its position in the second trimer. MMPA-CoA has a similar binding mode to MTA-CoA in the first trimer. MMPA-CoA cannot be hydrated and is only hydrolyzed slowly by DmdD. Replacement of the sulfur atom in MMPA-CoA with a methylene group abolishes hydrolysis, suggesting that the unique property of the substrate is a major determinant of the hydrolysis activity of DmdD. | |||
Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA.,Tan D, Crabb WM, Whitman WB, Tong L PLoS One. 2013 May 21;8(5):e63870. doi: 10.1371/journal.pone.0063870. Print 2013. PMID:23704947<ref>PMID:23704947</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4izb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Enoyl-CoA hydratase 3D structures|Enoyl-CoA hydratase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ruegeria pomeroyi DSS-3]] | |||
[[Category: Tan D]] | |||
[[Category: Tong L]] | |||
Latest revision as of 18:34, 20 September 2023
Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoACrystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA
Structural highlights
FunctionDMDD_RUEPO Involved in the assimilation of dimethylsulphoniopropionate (DMSP), an important compound in the fixation of carbon in marine phytoplankton, by catalyzing both the hydration and the hydrolysis of 3-(methylthio)acryloyl-CoA (MTA-CoA) to acetaldehyde, CO2, MeSH, and CoA (PubMed:21562561, PubMed:23704947).[1] [2] Publication Abstract from PubMedDimethyl-sulphoniopropionate (DMSP) is produced in abundance by marine phytoplankton, and the catabolism of this compound is an important source of carbon and reduced sulfur for marine bacteria and other organisms. The enzyme DmdD catalyzes the last step in the methanethiol (MeSH) pathway of DMSP catabolism. DmdD is a member of the crotonase superfamily of enzymes, and it catalyzes both the hydration and the hydrolysis of methylthioacryloyl-CoA (MTA-CoA), converting it to acetaldehyde, CO2, MeSH, and CoA. We report here the crystal structure of Ruegeria pomeroyi DmdD free enzyme at 1.5 A resolution and the structures of the E121A mutant in complex with MTA-CoA and 3-methylmercaptopropionate-CoA (MMPA-CoA) at 1.8 A resolution. DmdD is a hexamer, composed of a dimer of trimers where the three monomers of each trimer are related by a crystallographic 3-fold axis. The overall structure of this hexamer is similar to those of canonical crotonases. However, the C-terminal loops of DmdD in one of the trimers assume a different conformation and contribute to CoA binding in the active site of a neighboring monomer of the trimer, while these loops in the second trimer are disordered. MTA-CoA is bound deep in the active site in the first trimer, but shows a 1.5 A shift in its position in the second trimer. MMPA-CoA has a similar binding mode to MTA-CoA in the first trimer. MMPA-CoA cannot be hydrated and is only hydrolyzed slowly by DmdD. Replacement of the sulfur atom in MMPA-CoA with a methylene group abolishes hydrolysis, suggesting that the unique property of the substrate is a major determinant of the hydrolysis activity of DmdD. Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA.,Tan D, Crabb WM, Whitman WB, Tong L PLoS One. 2013 May 21;8(5):e63870. doi: 10.1371/journal.pone.0063870. Print 2013. PMID:23704947[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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