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| | <StructureSection load='2yaj' size='340' side='right'caption='[[2yaj]], [[Resolution|resolution]] 1.81Å' scene=''> | | <StructureSection load='2yaj' size='340' side='right'caption='[[2yaj]], [[Resolution|resolution]] 1.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2yaj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_scatologenes"_weinberg_and_ginsbourg_1927 "bacillus scatologenes" weinberg and ginsbourg 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YAJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2yaj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_scatologenes Clostridium scatologenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YAJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4HP:4-HYDROXYPHENYLACETATE'>4HP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.813Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y8n|2y8n]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4HP:4-HYDROXYPHENYLACETATE'>4HP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxyphenylacetate_decarboxylase 4-hydroxyphenylacetate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.83 4.1.1.83] </span></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=2yaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yaj OCA], [https://pdbe.org/2yaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yaj RCSB], [https://www.ebi.ac.uk/pdbsum/2yaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yaj ProSAT]</span></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=2yaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yaj OCA], [https://pdbe.org/2yaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yaj RCSB], [https://www.ebi.ac.uk/pdbsum/2yaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yaj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/HPDL_CLOSL HPDL_CLOSL] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus scatologenes weinberg and ginsbourg 1927]] | + | [[Category: Clostridium scatologenes]] |
| - | [[Category: 4-hydroxyphenylacetate decarboxylase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Blaser, M]] | + | [[Category: Blaser M]] |
| - | [[Category: Feliks, M]] | + | [[Category: Feliks M]] |
| - | [[Category: Martins, B M]] | + | [[Category: Martins BM]] |
| - | [[Category: Selmer, T]] | + | [[Category: Selmer T]] |
| - | [[Category: Ullmann, G M]] | + | [[Category: Ullmann GM]] |
| - | [[Category: Iron-sulfur center]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Radical chemistry]]
| + | |
| Structural highlights
Function
HPDL_CLOSL
Publication Abstract from PubMed
4-Hydroxyphenylacetate decarboxylase is a [4Fe-4S] cluster containing glycyl radical enzyme proposed to use a glycyl/thiyl radical dyad to catalyze the last step of tyrosine fermentation in clostridia. The decarboxylation product p-cresol (4-methylphenol) is a virulence factor of the human pathogen Clostridium difficile . Here we describe the crystal structures at 1.75 and 1.81 A resolution of substrate-free and substrate-bound 4-hydroxyphenylacetate decarboxylase from the related Clostridium scatologenes . The structures show a (betagamma)(4) tetramer of heterodimers composed of a catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters at 40 A distance from the active site. The gamma-subunit comprises two domains displaying pseudo-2-fold symmetry that are structurally related to the [4Fe-4S] cluster-binding scaffold of high-potential iron-sulfur proteins. The N-terminal domain coordinates one cluster with one histidine and three cysteines, and the C-terminal domain coordinates the second cluster with four cysteines. Whereas the C-terminal cluster is buried in the betagamma heterodimer interface, the N-terminal cluster is not part of the interface. The previously postulated decarboxylation mechanism required the substrate's hydroxyl group in the vicinity of the active cysteine residue. In contrast to expectation, the substrate-bound state shows a direct interaction between the substrate's carboxyl group and the active site Cys503, while His536 and Glu637 at the opposite side of the active site pocket anchor the hydroxyl group. This state captures a possible catalytically competent complex and suggests a Kolbe-type decarboxylation for p-cresol formation.
Structural basis for a kolbe-type decarboxylation catalyzed by a glycyl radical enzyme.,Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T J Am Chem Soc. 2011 Sep 21;133(37):14666-74. Epub 2011 Aug 26. PMID:21823587[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T. Structural basis for a kolbe-type decarboxylation catalyzed by a glycyl radical enzyme. J Am Chem Soc. 2011 Sep 21;133(37):14666-74. Epub 2011 Aug 26. PMID:21823587 doi:10.1021/ja203344x
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