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==Structure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domains==
==Structure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domains==
<StructureSection load='4qcc' size='340' side='right' caption='[[4qcc]], [[Resolution|resolution]] 7.08&Aring;' scene=''>
<StructureSection load='4qcc' size='340' side='right'caption='[[4qcc]], [[Resolution|resolution]] 7.08&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4qcc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QCC FirstGlance]. <br>
<table><tr><td colspan='2'>[[4qcc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QCC FirstGlance]. <br>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-dehydro-3-deoxy-6-phosphogalactonate_aldolase 2-dehydro-3-deoxy-6-phosphogalactonate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.21 4.1.2.21] </span></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]] 7.078&#8491;</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=4qcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qcc RCSB], [http://www.ebi.ac.uk/pdbsum/4qcc PDBsum]</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=4qcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcc OCA], [https://pdbe.org/4qcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qcc RCSB], [https://www.ebi.ac.uk/pdbsum/4qcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qcc ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DGOA_ECOLI DGOA_ECOLI]] Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.<ref>PMID:324806</ref> <ref>PMID:17981470</ref>
[https://www.uniprot.org/uniprot/DGOA_ECOLI DGOA_ECOLI] Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.<ref>PMID:324806</ref> <ref>PMID:17981470</ref> [https://www.uniprot.org/uniprot/FKBA_ECOLI FKBA_ECOLI] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here, we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 A diameter, cube-shaped cage with large openings into a 130 A diameter inner cavity. A crystal structure of the cage showed atomic-level agreement with the designed model, while electron microscopy, native mass spectrometry and small angle X-ray scattering revealed alternative assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will probably require limiting flexibility to select against alternative forms. These results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.
 
Structure of a designed protein cage that self-assembles into a highly porous cube.,Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO Nat Chem. 2014 Dec;6(12):1065-71. doi: 10.1038/nchem.2107. Epub 2014 Nov 10. PMID:25411884<ref>PMID:25411884</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Aldolase 3D structures|Aldolase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase]]
[[Category: Escherichia coli]]
[[Category: Lai, Y T]]
[[Category: Large Structures]]
[[Category: Yeates, T O]]
[[Category: Lai Y-T]]
[[Category: Bionanotechnology]]
[[Category: Yeates TO]]
[[Category: Lyase]]
[[Category: Porous biomaterial]]
[[Category: Protein design]]
[[Category: Self-assembly]]
[[Category: Structural protein]]
[[Category: Symmetry]]

Latest revision as of 15:45, 1 March 2024

Structure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domainsStructure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domains

Structural highlights

4qcc is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 7.078Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DGOA_ECOLI Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.[1] [2] FKBA_ECOLI PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

See Also

References

  1. ↑ Deacon J, Cooper RA. D-Galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli. FEBS Lett. 1977 May 15;77(2):201-5. PMID:324806
  2. ↑ Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Characterization and crystal structure of Escherichia coli KDPGal aldolase. Bioorg Med Chem. 2008 Jan 15;16(2):710-20. Epub 2007 Oct 18. PMID:17981470 doi:10.1016/j.bmc.2007.10.043

4qcc, resolution 7.08Å

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