4di8

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Revision as of 14:32, 11 August 2016

CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5

Structural highlights

4di8 is a 2 chain structure with sequence from "bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890. This structure supersedes the now removed PDB entry 4d95. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	2qah, 4d8l, 4di9, 4dia
Gene:	ligI ("Bacillus devorans" Zimmermann 1890)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PDCH_SPHPI] Plays an important role in the metabolism of lignin-derived aromatic compounds. Involved in the meta fission degradative pathway of protocatechuate. Catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to a mixture of 4-carboxy-2-hydroxymuconate (CHM) and 4-oxalomesaconate (OMA). The product of the enzymatic reaction exists in two forms depending on the pH. At pH 10, the keto form (OMA) is predominant, and at pH 6, the enol form (CHM) is predominant (PubMed:22475079).^[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
↑ Kersten PJ, Dagley S, Whittaker JW, Arciero DM, Lipscomb JD. 2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species. J Bacteriol. 1982 Dec;152(3):1154-62. PMID:7142106
↑ 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

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/4di8"

@@ 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==
 <StructureSection load='4di8' size='340' side='right' caption='[[4di8]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
 == 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 [http://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. 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>
 </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>
 <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='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='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 "Bacillus devorans" Zimmermann 1890])</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>
+<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://pdbe.org/4di8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4di8 RCSB], [http://www.ebi.ac.uk/pdbsum/4di8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4di8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/PDCH_SPHPI PDCH_SPHPI]] Plays an important role in the metabolism of lignin-derived aromatic compounds. Involved in the meta fission degradative pathway of protocatechuate. Catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to a mixture of 4-carboxy-2-hydroxymuconate (CHM) and 4-oxalomesaconate (OMA). The product of the enzymatic reaction exists in two forms depending on the pH. At pH 10, the keto form (OMA) is predominant, and at pH 6, the enol form (CHM) is predominant (PubMed:22475079).<ref>PMID:22475079</ref> <ref>PMID:7142106</ref> <ref>PMID:9864312</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4di8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Sphingomonas paucimobilis]]
+[[Category: Bacillus devorans zimmermann 1890]]
 [[Category: Almo, S C]]
 [[Category: Hobbs, M E]]

4di8

From Proteopedia

Revision as of 14:32, 11 August 2016

CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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