|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5== | | ==CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5== |
| - | <StructureSection load='4di8' size='340' side='right' caption='[[4di8]], [[Resolution|resolution]] 1.81Å' scene=''> | + | <StructureSection load='4di8' size='340' side='right'caption='[[4di8]], [[Resolution|resolution]] 1.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4di8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4d95 4d95]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DI8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4di8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DI8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0GY:(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLIC+ACID'>0GY</scene>, <scene name='pdbligand=0GZ:2-OXO-2H-PYRAN-4,6-DICARBOXYLIC+ACID'>0GZ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.81Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qah|2qah]], [[4d8l|4d8l]], [[4di9|4di9]], [[4dia|4dia]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0GY:(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLIC+ACID'>0GY</scene>, <scene name='pdbligand=0GZ:2-OXO-2H-PYRAN-4,6-DICARBOXYLIC+ACID'>0GZ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ligI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 Sphingomonas paucimobilis])</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=4di8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4di8 OCA], [https://pdbe.org/4di8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4di8 RCSB], [https://www.ebi.ac.uk/pdbsum/4di8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4di8 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=4di8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4di8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4di8 RCSB], [http://www.ebi.ac.uk/pdbsum/4di8 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/LIGI_SPHSK LIGI_SPHSK] Contributes to the degradation of lignin at the level of the protocatechuate 4,5-cleavage pathway (PubMed:9864312). Catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to (4E)-oxalomesaconate (OMA) (PubMed:22475079, PubMed:29658701). The keto form of OMA can tautomerize into the enol form, 4-carboxy-2-hydroxymuconate (CHM), under certain pH conditions (PubMed:22475079). Also catalyzes the reverse reaction (PubMed:22475079, PubMed:9864312). Is essential for the growth of Sphingobium sp. SYK-6 on vanillate but is not responsible for the growth of this strain on syringate (PubMed:9864312).<ref>PMID:22475079</ref> <ref>PMID:29658701</ref> <ref>PMID:9864312</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 16: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4di8" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Sphingomonas paucimobilis]] | | [[Category: Sphingomonas paucimobilis]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Hobbs, M E]] | + | [[Category: Hobbs ME]] |
| - | [[Category: Malashkevich, V N]] | + | [[Category: Malashkevich VN]] |
| - | [[Category: Raushel, F M]] | + | [[Category: Raushel FM]] |
| - | [[Category: Toro, R]] | + | [[Category: Toro R]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
LIGI_SPHSK Contributes to the degradation of lignin at the level of the protocatechuate 4,5-cleavage pathway (PubMed:9864312). Catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to (4E)-oxalomesaconate (OMA) (PubMed:22475079, PubMed:29658701). The keto form of OMA can tautomerize into the enol form, 4-carboxy-2-hydroxymuconate (CHM), under certain pH conditions (PubMed:22475079). Also catalyzes the reverse reaction (PubMed:22475079, PubMed:9864312). Is essential for the growth of Sphingobium sp. SYK-6 on vanillate but is not responsible for the growth of this strain on syringate (PubMed:9864312).[1] [2] [3]
Publication Abstract from PubMed
LigI from Sphingomonas paucimobilis catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to 4-oxalomesaconate and 4-carboxy-2-hydroxymuconate in the degradation of lignin. This protein is a member of the amidohydrolase superfamily of enzymes. The protein was expressed in Escherichia coli and then purified to homogeneity. The purified recombinant enzyme does not contain bound metal ions, and the addition of metal chelators or divalent metal ions to the assay mixtures does not affect the rate of product formation. This is the first enzyme from the amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity. The kinetic constants for the hydrolysis of PDC are 340 s(-1) and 9.8 x 10(6) M(-1) s(-1) (k(cat) and k(cat)/K(m), respectively). The pH dependence on the kinetic constants suggests that a single active site residue must be deprotonated for the hydrolysis of PDC. The site of nucleophilic attack was determined by conducting the hydrolysis of PDC in (18)O-labeled water and subsequent (13)C nuclear magnetic resonance analysis. The crystal structures of wild-type LigI and the D248A mutant in the presence of the reaction product were determined to a resolution of 1.9 A. The C-8 and C-11 carboxylate groups of PDC are coordinated within the active site via ion pair interactions with Arg-130 and Arg-124, respectively. The hydrolytic water molecule is activated by the transfer of a proton to Asp-248. The carbonyl group of the lactone substrate is activated by electrostatic interactions with His-180, His-31, and His-33.
Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation.,Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM Biochemistry. 2012 Apr 9. PMID:22475079[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM. Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation. Biochemistry. 2012 Apr 9. PMID:22475079 doi:http://dx.doi.org/10.1021/bi300307b
- ↑ Hogancamp TN, Raushel FM. Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6. Biochemistry. 2018 May 15;57(19):2837-2845. doi: 10.1021/acs.biochem.8b00295., Epub 2018 Apr 27. PMID:29658701 doi:http://dx.doi.org/10.1021/acs.biochem.8b00295
- ↑ Masai E, Shinohara S, Hara H, Nishikawa S, Katayama Y, Fukuda M. Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6. J Bacteriol. 1999 Jan;181(1):55-62. PMID:9864312
- ↑ Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM. Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation. Biochemistry. 2012 Apr 9. PMID:22475079 doi:http://dx.doi.org/10.1021/bi300307b
|
