6suw

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant

Structural highlights

6suw is a 30 chain structure with sequence from Rhodospirillum rubrum ATCC 11170. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.66Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FER_RHORT Cargo protein of a type 1 encapsulin nanocompartment. A ferritin-like ferroxidase that mineralizes iron inside the encapsulin nanocompartment. Converts Fe(2+) to Fe(3+) that is released to the exterior of the decameric complex for deposition in the encapsulin nanocompartment. In solution the decamer binds 10-15 iron cations; in the encapsulin nanocompartment the decamer can bind up to 48 ions, perhaps via its internal channel and on its exterior. The empty encapsulin nanocompartment sequesters about 2200 Fe ions while the cargo-loaded nanocompartment can maximally sequester about 4150 Fe ions. EncFtn retains ferroxidase activity when encapsulated (PubMed:27529188). Flux in the active site di-iron metal center is thought to be controlled by the 'entry site' of the protein, which both attracts metal and controls the rate of iron oxidation (Probable). Encapsulation in the nanocompartment does not alter either function of this protein (PubMed:32878987).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Encapsulated ferritins belong to the universally distributed ferritin superfamily, which function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question, due to differences in organization of the ferroxidase catalytic site and neighboring secondary metal binding sites. We have previously identified a putative metal binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron entry site by means of enzymatic assays, mass-spectrometry, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, while enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.

Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins.,Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Basle A, Waldron KJ, Clarke DJ, Marles-Wright J J Biol Chem. 2020 Sep 2. pii: RA120.014502. doi: 10.1074/jbc.RA120.014502. PMID:32878987^[4]

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

References

↑ He D, Hughes S, Vanden-Hehir S, Georgiev A, Altenbach K, Tarrant E, Mackay CL, Waldron KJ, Clarke DJ, Marles-Wright J. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. Elife. 2016 Aug 16;5. pii: e18972. doi: 10.7554/eLife.18972. PMID:27529188 doi:http://dx.doi.org/10.7554/eLife.18972
↑ Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Basle A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem. 2020 Sep 2. pii: RA120.014502. doi: 10.1074/jbc.RA120.014502. PMID:32878987 doi:http://dx.doi.org/10.1074/jbc.RA120.014502
↑ Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Basle A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem. 2020 Sep 2. pii: RA120.014502. doi: 10.1074/jbc.RA120.014502. PMID:32878987 doi:http://dx.doi.org/10.1074/jbc.RA120.014502
↑ Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Basle A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem. 2020 Sep 2. pii: RA120.014502. doi: 10.1074/jbc.RA120.014502. PMID:32878987 doi:http://dx.doi.org/10.1074/jbc.RA120.014502

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Large Structures | Rhodospirillum rubrum ATCC 11170 | He D | Marles-Wright J

@@ Line 3: / Line 3: @@
 <StructureSection load='6suw' size='340' side='right'caption='[[6suw]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6suw]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhort Rhort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SUW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SUW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6suw]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum_ATCC_11170 Rhodospirillum rubrum ATCC 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SUW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SUW FirstGlance]. <br>
-</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=FE:FE+(III)+ION'>FE</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]] 2.66&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rru_A0973 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269796 RHORT])</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=FE:FE+(III)+ION'>FE</scene></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=6suw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6suw OCA], [http://pdbe.org/6suw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6suw RCSB], [http://www.ebi.ac.uk/pdbsum/6suw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6suw 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=6suw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6suw OCA], [https://pdbe.org/6suw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6suw RCSB], [https://www.ebi.ac.uk/pdbsum/6suw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6suw ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER_RHORT FER_RHORT] Cargo protein of a type 1 encapsulin nanocompartment. A ferritin-like ferroxidase that mineralizes iron inside the encapsulin nanocompartment. Converts Fe(2+) to Fe(3+) that is released to the exterior of the decameric complex for deposition in the encapsulin nanocompartment. In solution the decamer binds 10-15 iron cations; in the encapsulin nanocompartment the decamer can bind up to 48 ions, perhaps via its internal channel and on its exterior. The empty encapsulin nanocompartment sequesters about 2200 Fe ions while the cargo-loaded nanocompartment can maximally sequester about 4150 Fe ions. EncFtn retains ferroxidase activity when encapsulated (PubMed:27529188). Flux in the active site di-iron metal center is thought to be controlled by the 'entry site' of the protein, which both attracts metal and controls the rate of iron oxidation (Probable). Encapsulation in the nanocompartment does not alter either function of this protein (PubMed:32878987).<ref>PMID:27529188</ref> <ref>PMID:32878987</ref> <ref>PMID:32878987</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Rhort]]
+[[Category: Rhodospirillum rubrum ATCC 11170]]
-[[Category: He, D]]
+[[Category: He D]]
-[[Category: Marles-Wright, J]]
+[[Category: Marles-Wright J]]
-[[Category: Encapsulated ferritin]]
-[[Category: Ferritin]]
-[[Category: Ferroxidase]]
-[[Category: Oxidoreductase]]

6suw

From Proteopedia

Current revision

Crystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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