View source for 7di1


==Crystal structure of the rationally designed mkDPBB_sym_86 protein==
<StructureSection load='7di1' size='340' side='right'caption='[[7di1]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7di1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.097&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
The extant complex proteins must have evolved from ancient short and simple ancestors. The double-psi beta-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.,Yagi S, Padhi AK, Vucinic J, Barbe S, Schiex T, Nakagawa R, Simoncini D, Zhang KYJ, Tagami S J Am Chem Soc. 2021 Oct 6;143(39):15998-16006. doi: 10.1021/jacs.1c05367. Epub, 2021 Sep 24. PMID:34559526<ref>PMID:34559526</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 7di1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Tagami S]]
[[Category: Yagi S]]