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| | <StructureSection load='6n99' size='340' side='right'caption='[[6n99]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='6n99' size='340' side='right'caption='[[6n99]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6n99]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._f-1 Streptomyces sp. f-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N99 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N99 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6n99]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._f-1 Streptomyces sp. f-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N99 FirstGlance]. <br> |
| | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylA_1, xylA, STEPF1_01030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=463642 Streptomyces sp. F-1])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylA_1, xylA, STEPF1_01030 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=463642 Streptomyces sp. F-1])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6n99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n99 OCA], [http://pdbe.org/6n99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n99 RCSB], [http://www.ebi.ac.uk/pdbsum/6n99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n99 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=6n99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n99 OCA], [https://pdbe.org/6n99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n99 RCSB], [https://www.ebi.ac.uk/pdbsum/6n99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n99 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Structural highlights
6n99 is a 4 chain structure with sequence from Streptomyces sp. f-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , |
| Gene: | xylA_1, xylA, STEPF1_01030 (Streptomyces sp. F-1) |
| Activity: | Xylose isomerase, with EC number 5.3.1.5 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
BACKGROUND: Enzymatic isomerization is a promising strategy to solve the problem of xylose fermentation and, consequently, to leverage the production of advanced biofuels and biochemicals. In a previous work, our research group discovered a new strain of Streptomyces with great biotechnological potential due to its ability to produce a broad arsenal of enzymes related to lignocellulose degradation. METHODS: We applied a multidisciplinary approach involving enzyme kinetics, biophysical methods, small angle X-ray scattering and X-ray crystallography to investigate two novel xylose isomerases, XylA1F1 and XylA2F1, from this strain. RESULTS: We showed that while XylA1F1 prefers to act at lower temperatures and relatively lower pH, XylA2F1 is extremely stable at higher temperatures and presents a higher turnover number. Structural analysis revealed that XylA1F1 exhibits unique properties in the active site not observed in classical XylAs from classes I and II nor in its ortholog XylA2F1. It encompasses the natural substitutions, M86A and T93K, that create an extra room for substrate accommodation and narrow the active-site entrance, respectively. Such modifications may contribute to the functional differentiation of these enzymes. CONCLUSIONS: We have characterized two novel xylose isomerases that display distinct functional behavior and harbor unprecedented amino-acid substitutions in the catalytic interface. GENERAL SIGNIFICANCE: Our findings contribute to a better understanding of the functional and structural aspects of xylose isomerases, which might be instrumental for the valorization of the hemicellulosic fraction of vegetal biomass.
Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes.,Miyamoto RY, de Sousa AS, Vieira PS, de Melo RR, Scarpassa JA, Ramos CHI, Murakami MT, Ruller R, Zanphorlin LM Biochim Biophys Acta Gen Subj. 2020 May;1864(5):129549. doi:, 10.1016/j.bbagen.2020.129549. Epub 2020 Feb 5. PMID:32035160[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Miyamoto RY, de Sousa AS, Vieira PS, de Melo RR, Scarpassa JA, Ramos CHI, Murakami MT, Ruller R, Zanphorlin LM. Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes. Biochim Biophys Acta Gen Subj. 2020 May;1864(5):129549. doi:, 10.1016/j.bbagen.2020.129549. Epub 2020 Feb 5. PMID:32035160 doi:http://dx.doi.org/10.1016/j.bbagen.2020.129549
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