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| | ==Crystal structure of Slr0204, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Synechocystis== | | ==Crystal structure of Slr0204, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Synechocystis== |
| - | <StructureSection load='4k00' size='340' side='right' caption='[[4k00]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='4k00' size='340' side='right'caption='[[4k00]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k00]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K00 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K00 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k00]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K00 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k02|4k02]]</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=4k00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k00 OCA], [https://pdbe.org/4k00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k00 RCSB], [https://www.ebi.ac.uk/pdbsum/4k00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k00 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">slr0204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_hydrolase 1,4-dihydroxy-2-naphthoyl-CoA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.28 3.1.2.28] </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=4k00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k00 OCA], [http://pdbe.org/4k00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k00 RCSB], [http://www.ebi.ac.uk/pdbsum/4k00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k00 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DNCH_SYNY3 DNCH_SYNY3]] Catalyzes the specific hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis. Is not active on benzoyl-CoA, phenylacetyl-CoA and aliphatic acyl-CoA thioesters.<ref>PMID:19321747</ref> | + | [https://www.uniprot.org/uniprot/DNCH_SYNY3 DNCH_SYNY3] Catalyzes the specific hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis. Is not active on benzoyl-CoA, phenylacetyl-CoA and aliphatic acyl-CoA thioesters.<ref>PMID:19321747</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Thioesterase|Thioesterase]] | + | *[[Thioesterase 3D structures|Thioesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Syny3]] | + | [[Category: Synechocystis sp. PCC 6803 substr. Kazusa]] |
| - | [[Category: Allen, W J]] | + | [[Category: Allen WJ]] |
| - | [[Category: Basset, G]] | + | [[Category: Basset G]] |
| - | [[Category: Furt, F]] | + | [[Category: Furt F]] |
| - | [[Category: Madzelan, P]] | + | [[Category: Madzelan P]] |
| - | [[Category: Rizzo, R C]] | + | [[Category: Rizzo RC]] |
| - | [[Category: Widhalm, J R]] | + | [[Category: Widhalm JR]] |
| - | [[Category: Wilson, M A]] | + | [[Category: Wilson MA]] |
| - | [[Category: Hotdog fold]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Thioesterase]]
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| Structural highlights
Function
DNCH_SYNY3 Catalyzes the specific hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis. Is not active on benzoyl-CoA, phenylacetyl-CoA and aliphatic acyl-CoA thioesters.[1]
Publication Abstract from PubMed
The synthesis of phylloquinone (vitamin K1) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to release 1,4-dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacterium Synechocystis (Slr0204) and the flowering plant Arabidopsis thaliana (AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNA-CoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases from Pseudomonas and Arthrobacter. Like the 4-HBA-CoA thioesterases, the DHNA-CoA thioesterases contain either an active-site aspartate (Slr0204) or glutamate (AtDHNAT1) that are predicted to be catalytically important. Computational modeling of the substrate-bound forms of both enzymes indicates the residues that are likely to be involved in substrate binding and catalysis. Both enzymes are selective for DHNA-CoA as a substrate, but this selectivity is achieved using divergent predicted binding strategies. The Slr0204 binding pocket is predominantly hydrophobic and closely conforms to DHNA, while that of AtDHNAT1 is more polar and solvent-exposed. Considered in light of the related 4-HBA-CoA thioesterases, these structures indicate that hotdog-fold thioesterases using either an active-site aspartate or glutamate diverged into distinct clades prior to the evolution of strong substrate specificity in these enzymes.
Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis.,Furt F, Allen WJ, Widhalm JR, Madzelan P, Rizzo RC, Basset G, Wilson MA Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1876-88. doi:, 10.1107/S0907444913015771. Epub 2013 Sep 20. PMID:24100308[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Widhalm JR, van Oostende C, Furt F, Basset GJ. A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5599-603. doi:, 10.1073/pnas.0900738106. Epub 2009 Mar 25. PMID:19321747 doi:10.1073/pnas.0900738106
- ↑ Furt F, Allen WJ, Widhalm JR, Madzelan P, Rizzo RC, Basset G, Wilson MA. Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis. Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1876-88. doi:, 10.1107/S0907444913015771. Epub 2013 Sep 20. PMID:24100308 doi:http://dx.doi.org/10.1107/S0907444913015771
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