|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Arabidopsis thaliana== | | ==Crystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Arabidopsis thaliana== |
| - | <StructureSection load='4k02' size='340' side='right' caption='[[4k02]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='4k02' size='340' side='right'caption='[[4k02]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k02]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K02 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k02]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K02 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k00|4k00]]</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]] 1.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g48320, F11A17.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4k02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k02 OCA], [https://pdbe.org/4k02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k02 RCSB], [https://www.ebi.ac.uk/pdbsum/4k02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k02 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=4k02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k02 OCA], [http://pdbe.org/4k02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k02 RCSB], [http://www.ebi.ac.uk/pdbsum/4k02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k02 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DNAT1_ARATH DNAT1_ARATH] Catalyzes the hydrolysis of the thioester bond of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) in peroxisomes, a necessary step to form the naphthoquinone ring of phylloquinone (vitamin K(1)). Is not active on benzoyl-CoA, phenylacetyl-CoA, succinyl-CoA and palmitoyl-CoA thioesters.<ref>PMID:22372525</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 19: |
Line 20: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Thioesterase|Thioesterase]] | + | *[[Thioesterase 3D structures|Thioesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Allen, W J]] | + | [[Category: Large Structures]] |
| - | [[Category: Basset, G]] | + | [[Category: Allen WJ]] |
| - | [[Category: Furt, F]] | + | [[Category: Basset G]] |
| - | [[Category: Madzelan, P]] | + | [[Category: Furt F]] |
| - | [[Category: Rizzo, R C]] | + | [[Category: Madzelan P]] |
| - | [[Category: Widhalm, J R]] | + | [[Category: Rizzo RC]] |
| - | [[Category: Wilson, M A]] | + | [[Category: Widhalm JR]] |
| - | [[Category: Hotdog fold]]
| + | [[Category: Wilson MA]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Thioesterase]]
| + | |
| Structural highlights
Function
DNAT1_ARATH Catalyzes the hydrolysis of the thioester bond of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) in peroxisomes, a necessary step to form the naphthoquinone ring of phylloquinone (vitamin K(1)). Is not active on benzoyl-CoA, phenylacetyl-CoA, succinyl-CoA and palmitoyl-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, Ducluzeau AL, Buller NE, Elowsky CG, Olsen LJ, Basset GJ. Phylloquinone (vitamin K(1) ) biosynthesis in plants: two peroxisomal thioesterases of Lactobacillales origin hydrolyze 1,4-dihydroxy-2-naphthoyl-CoA. Plant J. 2012 Jul;71(2):205-15. doi: 10.1111/j.1365-313X.2012.04972.x. Epub 2012 , Jun 19. PMID:22372525 doi:http://dx.doi.org/10.1111/j.1365-313X.2012.04972.x
- ↑ 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
|
