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| | ==Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) wild type== | | ==Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) wild type== |
| - | <StructureSection load='5gu8' size='340' side='right' caption='[[5gu8]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='5gu8' size='340' side='right'caption='[[5gu8]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gu8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GU8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GU8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gu8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GU8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gu9|5gu9]], [[5gua|5gua]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1284 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=5gu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gu8 OCA], [https://pdbe.org/5gu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gu8 RCSB], [https://www.ebi.ac.uk/pdbsum/5gu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gu8 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=5gu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gu8 OCA], [http://pdbe.org/5gu8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gu8 RCSB], [http://www.ebi.ac.uk/pdbsum/5gu8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gu8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/O59021_PYRHO O59021_PYRHO] |
| | <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: Pyrococcus horikoshii]] | + | [[Category: Large Structures]] |
| - | [[Category: Fukasawa, Y]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Kunishima, N]] | + | [[Category: Fukasawa Y]] |
| - | [[Category: Matsuura, Y]] | + | [[Category: Kunishima N]] |
| - | [[Category: Naitow, H]] | + | [[Category: Matsuura Y]] |
| - | [[Category: Nakai, K]] | + | [[Category: Naitow H]] |
| - | [[Category: Tomii, K]] | + | [[Category: Nakai K]] |
| - | [[Category: Yamada, K]] | + | [[Category: Tomii K]] |
| - | [[Category: Crystal contact engineering]]
| + | [[Category: Yamada K]] |
| - | [[Category: Crystal packing]]
| + | |
| - | [[Category: Surface engineering]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
O59021_PYRHO
Publication Abstract from PubMed
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a beta-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for beta-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for beta-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a beta-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.
Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.,Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):757-766. doi:, 10.1107/S2059798317010932. Epub 2017 Aug 15. PMID:28876239[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):757-766. doi:, 10.1107/S2059798317010932. Epub 2017 Aug 15. PMID:28876239 doi:http://dx.doi.org/10.1107/S2059798317010932
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