5xgo: Difference between revisions

Latest revision as of 10:18, 27 March 2024

The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the Crystal Structure of a Maxi-/Mini-Ferritin Chimera

Structural highlights

5xgo is a 12 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.99Å
Ligands:	CL
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BFR_ECOLI Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.^[1] ^[2] DPS_ECOLI During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.^[3] ^[4] ^[5] ^[6]

References

↑ Yang X, Le Brun NE, Thomson AJ, Moore GR, Chasteen ND. The iron oxidation and hydrolysis chemistry of Escherichia coli bacterioferritin. Biochemistry. 2000 Apr 25;39(16):4915-23. PMID:10769150
↑ Baaghil S, Lewin A, Moore GR, Le Brun NE. Core formation in Escherichia coli bacterioferritin requires a functional ferroxidase center. Biochemistry. 2003 Dec 2;42(47):14047-56. PMID:14636073 doi:https://dx.doi.org/10.1021/bi035253u
↑ Almiron M, Link AJ, Furlong D, Kolter R. A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 1992 Dec;6(12B):2646-54. PMID:1340475
↑ Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A. DNA protection by stress-induced biocrystallization. Nature. 1999 Jul 1;400(6739):83-5. PMID:10403254 doi:https://dx.doi.org/10.1038/21918
↑ Nair S, Finkel SE. Dps protects cells against multiple stresses during stationary phase. J Bacteriol. 2004 Jul;186(13):4192-8. PMID:15205421 doi:https://dx.doi.org/10.1128/JB.186.13.4192-4198.2004
↑ Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E. DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res. 2004 Nov 8;32(19):5935-44. Print 2004. PMID:15534364 doi:https://dx.doi.org/32/19/5935

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OCA

[1] Yang X, Le Brun NE, Thomson AJ, Moore GR, Chasteen ND. The iron oxidation and hydrolysis chemistry of Escherichia coli bacterioferritin. Biochemistry. 2000 Apr 25;39(16):4915-23. PMID:10769150

[2] Baaghil S, Lewin A, Moore GR, Le Brun NE. Core formation in Escherichia coli bacterioferritin requires a functional ferroxidase center. Biochemistry. 2003 Dec 2;42(47):14047-56. PMID:14636073 doi:https://dx.doi.org/10.1021/bi035253u

[3] Almiron M, Link AJ, Furlong D, Kolter R. A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 1992 Dec;6(12B):2646-54. PMID:1340475

[4] Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A. DNA protection by stress-induced biocrystallization. Nature. 1999 Jul 1;400(6739):83-5. PMID:10403254 doi:https://dx.doi.org/10.1038/21918

[5] Nair S, Finkel SE. Dps protects cells against multiple stresses during stationary phase. J Bacteriol. 2004 Jul;186(13):4192-8. PMID:15205421 doi:https://dx.doi.org/10.1128/JB.186.13.4192-4198.2004

[6] Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E. DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res. 2004 Nov 8;32(19):5935-44. Print 2004. PMID:15534364 doi:https://dx.doi.org/32/19/5935

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='5xgo' size='340' side='right'caption='[[5xgo]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xgo]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XGO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xgo]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XGO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.99&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgo OCA], [http://pdbe.org/5xgo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xgo RCSB], [http://www.ebi.ac.uk/pdbsum/5xgo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgo ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5xgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgo OCA], [https://pdbe.org/5xgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xgo RCSB], [https://www.ebi.ac.uk/pdbsum/5xgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPS_ECOLI DPS_ECOLI]] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.<ref>PMID:1340475</ref> <ref>PMID:10403254</ref> <ref>PMID:15205421</ref> <ref>PMID:15534364</ref>
+[https://www.uniprot.org/uniprot/BFR_ECOLI BFR_ECOLI] Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule.<ref>PMID:10769150</ref> <ref>PMID:14636073</ref> [https://www.uniprot.org/uniprot/DPS_ECOLI DPS_ECOLI] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.<ref>PMID:1340475</ref> <ref>PMID:10403254</ref> <ref>PMID:15205421</ref> <ref>PMID:15534364</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cage proteins assemble into nanoscale structures with large central cavities. They play roles, including those as virus capsids and chaperones, and have been applied to drug delivery and nanomaterials. Furthermore, protein cages have been used as model systems to understand and design protein quaternary structure. Ferritins are ubiquitous protein cages that manage iron homeostasis and oxidative damage. Two ferritin subfamilies have strongly similar tertiary structure yet distinct quaternary structure: maxi-ferritins normally assemble into 24-meric, octahedral cages with C-terminal E-helices centered around 4-fold symmetry axes, and mini-ferritins are 12-meric, tetrahedral cages with 3-fold axes defined by C-termini lacking E-domains. To understand the role E-domains play in ferritin quaternary structure, we previously designed a chimera of a maxi-ferritin E-domain fused to the C-terminus of a mini-ferritin. The chimera is a 12-mer cage midway in size between those of the maxi- and mini-ferritin. The research described herein sets out to understand (a) whether the increase in size over a typical mini-ferritin is due to a frozen state where the E-domain is flipped out of the cage and (b) whether the symmetrical preference of the E-domain in the maxi-ferritin (4-fold axis) overrules the C-terminal preference in the mini-ferritin (3-fold axis). With a 1.99 A resolution crystal structure, we determined that the chimera assembles into a tetrahedral cage that can be nearly superimposed with the parent mini-ferritin, and that the E-domains are flipped external to the cage at the 3-fold symmetry axes.
-The Crystal Structure of a Maxi/Mini-Ferritin Chimera Reveals Guiding Principles for the Assembly of Protein Cages.,Cornell TA, Srivastava Y, Jauch R, Fan R, Orner BP Biochemistry. 2017 Aug 1;56(30):3894-3899. doi: 10.1021/acs.biochem.7b00312. Epub, 2017 Jul 21. PMID:28682051<ref>PMID:28682051</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5xgo" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 25: / Line 17: @@
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Cornell, T A]]
+[[Category: Cornell TA]]
-[[Category: Fan, R]]
+[[Category: Fan R]]
-[[Category: Jauch, R]]
+[[Category: Jauch R]]
-[[Category: Orner, B P]]
+[[Category: Orner BP]]
-[[Category: Srivastava, Y]]
+[[Category: Srivastava Y]]
-[[Category: Ferritin]]
-[[Category: Oxidoreductase]]
-[[Category: Protein cage]]
-[[Category: Protein engineering]]

5xgo: Difference between revisions

Latest revision as of 10:18, 27 March 2024

The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the Crystal Structure of a Maxi-/Mini-Ferritin Chimera

Structural highlights

Function

See Also

References

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