|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of L-arabinonate dehydratase in holo-form== | | ==Crystal structure of L-arabinonate dehydratase in holo-form== |
| - | <StructureSection load='5j84' size='340' side='right' caption='[[5j84]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='5j84' size='340' side='right'caption='[[5j84]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5j84]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhilw Rhilw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J84 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5j84]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobium_leguminosarum_bv._trifolii_WSM2304 Rhizobium leguminosarum bv. trifolii WSM2304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J84 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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]] 2.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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">Rleg2_2909 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW]), 6981653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW])</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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [https://pdbe.org/5j84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [https://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.9 4.2.1.9] </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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [http://pdbe.org/5j84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [http://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ARAD_RHILW ARAD_RHILW] Catalyzes the dehydration of L-arabinonate to 2-dehydro-3-deoxy-L-arabinonate during L-arabinose degradation. Can also dehydrate D-galactonate and D-fuconate with good catalytic efficiency. Has weak activity with D-xylonate and D-gluconate.<ref>PMID:27102126</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 23: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Rhilw]] | + | [[Category: Rhizobium leguminosarum bv. trifolii WSM2304]] |
| - | [[Category: Hakulinen, N]] | + | [[Category: Hakulinen N]] |
| - | [[Category: Rahman, M M]] | + | [[Category: Rahman MM]] |
| - | [[Category: Rouvinen, J]] | + | [[Category: Rouvinen J]] |
| - | [[Category: 2fe2s cluster]]
| + | |
| - | [[Category: L-arabinonate dehydratase]]
| + | |
| - | [[Category: L-arabonate dehydratase]]
| + | |
| - | [[Category: Pentonate dehydratase]]
| + | |
| Structural highlights
Function
ARAD_RHILW Catalyzes the dehydration of L-arabinonate to 2-dehydro-3-deoxy-L-arabinonate during L-arabinose degradation. Can also dehydrate D-galactonate and D-fuconate with good catalytic efficiency. Has weak activity with D-xylonate and D-gluconate.[1]
Publication Abstract from PubMed
We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg(2+) ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster.,Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttila M, Janis J, Koivula A, Rouvinen J, Hakulinen N ACS Chem Biol. 2017 Jul 21;12(7):1919-1927. doi: 10.1021/acschembio.7b00304. Epub, 2017 Jun 13. PMID:28574691[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Andberg M, Aro-Kärkkäinen N, Carlson P, Oja M, Bozonnet S, Toivari M, Hakulinen N, O'Donohue M, Penttilä M, Koivula A. Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases. Appl Microbiol Biotechnol. 2016 Sep;100(17):7549-63. PMID:27102126 doi:10.1007/s00253-016-7530-8
- ↑ Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttila M, Janis J, Koivula A, Rouvinen J, Hakulinen N. The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. ACS Chem Biol. 2017 Jul 21;12(7):1919-1927. doi: 10.1021/acschembio.7b00304. Epub, 2017 Jun 13. PMID:28574691 doi:http://dx.doi.org/10.1021/acschembio.7b00304
|
