4w4s
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4w4s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3w3h 3w3h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W4S FirstGlance]. <br> | <table><tr><td colspan='2'>[[4w4s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3w3h 3w3h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W4S FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B29:[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC+ACID'>B29</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]] 2Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B29:[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC+ACID'>B29</scene></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=4w4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w4s OCA], [https://pdbe.org/4w4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w4s RCSB], [https://www.ebi.ac.uk/pdbsum/4w4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w4s 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=4w4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w4s OCA], [https://pdbe.org/4w4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w4s RCSB], [https://www.ebi.ac.uk/pdbsum/4w4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w4s ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/Y2150_BRADU Y2150_BRADU] | [https://www.uniprot.org/uniprot/Y2150_BRADU Y2150_BRADU] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | We report the first X-ray crystal structure of ent-kaur-16-ene synthase from Bradyrhizobium japonicum, together with the results of a site-directed mutagenesis investigation into catalytic activity. The structure is very similar to that of the alpha domains of modern plant terpene cyclases, a result that is of interest since it has been proposed that many plant terpene cyclases may have arisen from bacterial diterpene cyclases. The ent-copalyl diphosphate substrate binds to a hydrophobic pocket near a cluster of Asp and Arg residues that are essential for catalysis, with the carbocations formed on ionization being protected by Leu, Tyr and Phe residues. A bisphosphonate inhibitor binds to the same site. In the kaurene synthase from the moss Physcomitrella patens, 16-alpha-hydroxy-ent-kaurane as well as kaurene are produced since Leu and Tyr in the P. patens kaurene synthase active site are replaced by smaller residues enabling carbocation quenching by water. Overall, the results represent the first structure determination of a bacterial diterpene cyclase, providing insights into catalytic activity, as well as structural comparisons with diverse terpene synthases and cyclases which clearly separate the terpene cyclases from other terpene synthases having highly alpha-helical structures. | ||
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| - | Structure, function and inhibition of ent-kaurene synthase from Bradyrhizobium japonicum.,Liu W, Feng X, Zheng Y, Huang CH, Nakano C, Hoshino T, Bogue S, Ko TP, Chen CC, Cui Y, Li J, Wang I, Hsu ST, Oldfield E, Guo RT Sci Rep. 2014 Oct 1;4:6214. doi: 10.1038/srep06214. PMID:25269599<ref>PMID:25269599</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4w4s" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal structure of ent-kaurene synthase BJKS from bradyrhizobium japonicum in complex with BPH-629
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