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6dhz

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Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines

Structural highlights

6dhz is a 4 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 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C562_ECOLX Electron-transport protein of unknown function.

Publication Abstract from PubMed

Despite significant progress in protein design, the construction of protein assemblies that display complex functions (e.g., catalysis or allostery) remains a significant challenge. We recently reported the de novo construction of an allosteric supramolecular protein assembly (Zn-C38/C81/C96R14) in which the dissociation and binding of Zn(II) ions were coupled over a distance of 15 A to the selective hydrolytic breakage and formation of a single disulfide bond. Zn4-C38/C81/C96R14 was constructed by ZnII-templated assembly of a monomeric protein (R1, a derivative of cytochrome cb562) into a tetramer, followed by progressive incorporation of non-covalent and disulfide bonding interactions into the protein-protein interfaces to create a strained quaternary architecture. The interfacial strain thus built allowed mechanical coupling between the binding/dissociation of Zn(II) and formation/hydrolysis of a single disulfide bond (C38-C38) out of a possible six. While the earlier study provided structural evidence for the two end-states of allosteric coupling, the energetic basis for allosteric coupling and the minimal structural requirements for building this allosteric system were not understood. Toward this end, we have characterized the structures and Zn-binding properties of two related protein con-structs (C38/C96R1 and C38R1) which also possess C38-C38 disulfide bonds. In addition, we have carried out extensive molecular dy-namics (MD) simulations of C38/C81/C96R14 to understand the energetic basis for the selective cleavage of the C38-C38 disulfide bond upon Zn(II) dissociation. Our analyses reveal that the local interfacial environment around the C38-C38 bond is key to its selective cleavage, but this cleavage is only possible within the context of a stable quaternary architecture which enables structural coupling between Zn(II) coordination and the protein-protein interfaces.

Determining the structural and energetic basis of allostery in a de novo designed metalloprotein assembly.,Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA J Am Chem Soc. 2018 Jul 12. doi: 10.1021/jacs.8b05812. PMID:29996654^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. Determining the structural and energetic basis of allostery in a de novo designed metalloprotein assembly. J Am Chem Soc. 2018 Jul 12. doi: 10.1021/jacs.8b05812. PMID:29996654 doi:http://dx.doi.org/10.1021/jacs.8b05812

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dhz"

Categories: Escherichia coli | Large Structures | Churchfield LA | Tezcan FA

@@ Line 1: / Line 1: @@
 ==Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines==
-<StructureSection load='6dhz' size='340' side='right' caption='[[6dhz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='6dhz' size='340' side='right'caption='[[6dhz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dhz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DHZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dhz]] is a 4 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=6DHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.8&#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=6dhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhz OCA], [http://pdbe.org/6dhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhz RCSB], [http://www.ebi.ac.uk/pdbsum/6dhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhz ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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=6dhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhz OCA], [https://pdbe.org/6dhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhz RCSB], [https://www.ebi.ac.uk/pdbsum/6dhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.
+[https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6dhz" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome b5 3D structures|Cytochrome b5 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Churchfield, L A]]
+[[Category: Escherichia coli]]
-[[Category: Tezcan, F A]]
+[[Category: Large Structures]]
-[[Category: 4-helix bundle]]
+[[Category: Churchfield LA]]
-[[Category: Electron transport]]
+[[Category: Tezcan FA]]
-[[Category: Engineered protein]]
-[[Category: Metalloprotein]]

6dhz

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Current revision

Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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