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| | <StructureSection load='2xhz' size='340' side='right'caption='[[2xhz]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='2xhz' size='340' side='right'caption='[[2xhz]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2xhz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2xhz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHZ FirstGlance]. <br> |
| - | </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arabinose-5-phosphate_isomerase Arabinose-5-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.13 5.3.1.13] </span></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]] 2.6Å</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=2xhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhz OCA], [https://pdbe.org/2xhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhz RCSB], [https://www.ebi.ac.uk/pdbsum/2xhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhz 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=2xhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhz OCA], [https://pdbe.org/2xhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhz RCSB], [https://www.ebi.ac.uk/pdbsum/2xhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhz ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/KDSD_ECOLI KDSD_ECOLI]] Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). KdsD is not essential in the KDO biosynthesis and can be substituted by GutQ. Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).<ref>PMID:12805358</ref> <ref>PMID:16199563</ref> <ref>PMID:16765569</ref>
| + | [https://www.uniprot.org/uniprot/KDSD_ECOLI KDSD_ECOLI] Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). KdsD is not essential in the KDO biosynthesis and can be substituted by GutQ. Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).<ref>PMID:12805358</ref> <ref>PMID:16199563</ref> <ref>PMID:16765569</ref> |
| | <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 coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Arabinose-5-phosphate isomerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bolognesi, M]] | + | [[Category: Bolognesi M]] |
| - | [[Category: Deho, G]] | + | [[Category: Deho G]] |
| - | [[Category: Gourlay, L J]] | + | [[Category: Gourlay LJ]] |
| - | [[Category: Nardini, M]] | + | [[Category: Nardini M]] |
| - | [[Category: Polissi, A]] | + | [[Category: Polissi A]] |
| - | [[Category: Sommaruga, S]] | + | [[Category: Sommaruga S]] |
| - | [[Category: Sperandeo, P]] | + | [[Category: Sperandeo P]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Lipopolysaccharide biogenesis]]
| + | |
| Structural highlights
Function
KDSD_ECOLI Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). KdsD is not essential in the KDO biosynthesis and can be substituted by GutQ. Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).[1] [2] [3]
Publication Abstract from PubMed
Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug-resistant bacteria. A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. API is composed of two main domains: an N-terminal sugar isomerase domain (SIS) and a pair of cystathionine-beta-synthase domains of unknown function. As the three-dimensional structure of an enzyme is a prerequisite for the rational development of novel inhibitors, we present here the crystal structure of the SIS domain of a catalytic mutant (K59A) of E. coli D-arabinose-5-phosphate isomerase at 2.6-A resolution. Our structural analyses and comparisons made with other SIS domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. On the basis of such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two-domain isomerases.
Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography.,Gourlay LJ, Sommaruga S, Nardini M, Sperandeo P, Deho G, Polissi A, Bolognesi M Protein Sci. 2010 Dec;19(12):2430-9. doi: 10.1002/pro.525. PMID:20954237[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Meredith TC, Woodard RW. Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase. J Biol Chem. 2003 Aug 29;278(35):32771-7. Epub 2003 Jun 12. PMID:12805358 doi:http://dx.doi.org/10.1074/jbc.M303661200
- ↑ Meredith TC, Woodard RW. Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase. J Bacteriol. 2005 Oct;187(20):6936-42. PMID:16199563 doi:http://dx.doi.org/10.1128/JB.187.20.6936-6942.2005
- ↑ Sperandeo P, Pozzi C, Deho G, Polissi A. Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus. Res Microbiol. 2006 Jul-Aug;157(6):547-58. Epub 2006 Feb 9. PMID:16765569 doi:10.1016/j.resmic.2005.11.014
- ↑ Gourlay LJ, Sommaruga S, Nardini M, Sperandeo P, Deho G, Polissi A, Bolognesi M. Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography. Protein Sci. 2010 Dec;19(12):2430-9. doi: 10.1002/pro.525. PMID:20954237 doi:10.1002/pro.525
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