5oyn: Difference between revisions

Latest revision as of 01:28, 28 December 2023

Crystal structure of D-xylonate dehydratase in holo-form

Structural highlights

5oyn is a 4 chain structure with sequence from Caulobacter vibrioides CB15. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	FES, KCX, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYLD_CAUVC Catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-arabinonate during D-xylose degradation. Can also dehydrate D-gluconate, with similar catalytic efficiency. Has weak activity with D-galactonate, D-fuconate and L-arabinonate.^[1]

Publication Abstract from PubMed

The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 A resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg(2+) ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.

The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family.,Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N Sci Rep. 2018 Jan 16;8(1):865. doi: 10.1038/s41598-018-19192-6. PMID:29339766^[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, Koivula A, Rouvinen J, Hakulinen N. The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. Sci Rep. 2018 Jan 16;8(1):865. doi: 10.1038/s41598-018-19192-6. PMID:29339766 doi:https://dx.doi.org/10.1038/s41598-018-19192-6

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N. The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. Sci Rep. 2018 Jan 16;8(1):865. doi: 10.1038/s41598-018-19192-6. PMID:29339766 doi:https://dx.doi.org/10.1038/s41598-018-19192-6

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Crystal structure of D-xylonate dehydratase in holo-form==
-<StructureSection load='5oyn' size='340' side='right' caption='[[5oyn]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='5oyn' size='340' side='right'caption='[[5oyn]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5oyn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OYN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5oyn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OYN 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]] 2.7&#8491;</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">CC_0819 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])</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=5oyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oyn OCA], [https://pdbe.org/5oyn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oyn RCSB], [https://www.ebi.ac.uk/pdbsum/5oyn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oyn 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=5oyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oyn OCA], [http://pdbe.org/5oyn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oyn RCSB], [http://www.ebi.ac.uk/pdbsum/5oyn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oyn ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYLD_CAUVC XYLD_CAUVC] Catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-arabinonate during D-xylose degradation. Can also dehydrate D-gluconate, with similar catalytic efficiency. Has weak activity with D-galactonate, D-fuconate and L-arabinonate.<ref>PMID:27102126</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Cauvc]]
+[[Category: Caulobacter vibrioides CB15]]
-[[Category: Hakulinen, N]]
+[[Category: Large Structures]]
-[[Category: Rahman, M M]]
+[[Category: Hakulinen N]]
-[[Category: Rouvinen, J]]
+[[Category: Rahman MM]]
-[[Category: D-xylonate dehydratase]]
+[[Category: Rouvinen J]]
-[[Category: Hydrolyase]]
-[[Category: Ilvd/edd enzyme]]
-[[Category: Lyase]]
-[[Category: Pentonate dehydratase]]

5oyn: Difference between revisions

Latest revision as of 01:28, 28 December 2023

Crystal structure of D-xylonate dehydratase in holo-form

Structural highlights

Function

Publication Abstract from PubMed

References

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