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| | ==Stationary phase survival protein E (SurE) from Xylella fastidiosa== | | ==Stationary phase survival protein E (SurE) from Xylella fastidiosa== |
| - | <StructureSection load='5ksq' size='340' side='right' caption='[[5ksq]], [[Resolution|resolution]] 2.63Å' scene=''> | + | <StructureSection load='5ksq' size='340' side='right'caption='[[5ksq]], [[Resolution|resolution]] 2.63Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ksq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KSQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ksq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xylella_fastidiosa_9a5c Xylella fastidiosa 9a5c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KSQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.63Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5ksq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksq OCA], [http://pdbe.org/5ksq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ksq RCSB], [http://www.ebi.ac.uk/pdbsum/5ksq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksq 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=5ksq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksq OCA], [https://pdbe.org/5ksq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ksq RCSB], [https://www.ebi.ac.uk/pdbsum/5ksq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SURE_XYLFA SURE_XYLFA]] Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. | + | [https://www.uniprot.org/uniprot/SURE_XYLFA SURE_XYLFA] Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. |
| | <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: 5'-nucleotidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Aparicio, R]] | + | [[Category: Xylella fastidiosa 9a5c]] |
| - | [[Category: Fonseca, E M.B]] | + | [[Category: Aparicio R]] |
| - | [[Category: Iulek, J]] | + | [[Category: De Souza AP]] |
| - | [[Category: Machado, A T.P]] | + | [[Category: De Toledo MA]] |
| - | [[Category: Polikarpov, I]] | + | [[Category: Dos Reis MA]] |
| - | [[Category: Reis, M A.Dos]] | + | [[Category: Dos Santos CA]] |
| - | [[Category: Santos, C A.Dos]]
| + | [[Category: Fonseca EMB]] |
| - | [[Category: Saraiva, A M]] | + | [[Category: Iulek J]] |
| - | [[Category: Souza, A P.De]] | + | [[Category: Machado ATP]] |
| - | [[Category: Toledo, M A.De]] | + | [[Category: Polikarpov I]] |
| - | [[Category: Crystallization]] | + | [[Category: Saraiva AM]] |
| - | [[Category: Hydrolase]] | + | |
| - | [[Category: Xylella fastidiosa]]
| + | |
| Structural highlights
Function
SURE_XYLFA Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates.
Publication Abstract from PubMed
Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein.
Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.,Machado ATP, Fonseca EMB, Reis MAD, Saraiva AM, Santos CAD, de Toledo MAS, Polikarpov I, de Souza AP, Aparicio R, Iulek J Proteins. 2017 Jul 5. doi: 10.1002/prot.25347. PMID:28677327[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Machado ATP, Fonseca EMB, Reis MAD, Saraiva AM, Santos CAD, de Toledo MAS, Polikarpov I, de Souza AP, Aparicio R, Iulek J. Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis. Proteins. 2017 Jul 5. doi: 10.1002/prot.25347. PMID:28677327 doi:http://dx.doi.org/10.1002/prot.25347
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