3gvy

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of bacterioferritin from R.sphaeroides

Structural highlights

3gvy is a 3 chain structure with sequence from Cereibacter sphaeroides 2.4.1. 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

Q3J696_CERS4 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.[PIRNR:PIRNR002560]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Iron is essential for the survival of organisms, but either excess or deficient levels of iron induce oxidative stress, thereby causing cell damage. As a result, iron regulation is essential for proper cell growth and proliferation in most organisms. Bacterioferritin is a ferritin-like family protein that contains a heme molecule and a ferroxidase site at the di-iron center. This protein plays a primary role in intracellular iron storage for iron homeostasis, as well as in the maintenance of iron in a soluble and non-toxic form. Although several bacterioferritin structures have been determined, no structural studies have successfully elucidated the molecular function of the heme molecule and the ferroxidase center. Here, we report the crystal structure of bacterioferritin from Rhodobacter sphaeroides. This protein exists in a roughly spherical configuration via the assembly of 24 subunits. We describe the oligomeric arrangement, ferroxidase center and heme-binding site based on this structure. The protein contains a single iron-binding configuration in the ferroxidase center, which allows for the release of iron by His130 when the protein is in the intermediate state. The heme molecule in RsBfr is stabilized by shifting of the van der Waals interaction center between the porphyrin of the heme and Trp26. We anticipate that further structural analysis will provide a more complete understanding of the molecular mechanisms of members of the ferritin-like family.

Crystal structure of bacterioferritin from Rhodobacter sphaeroides.,Nam KH, Xu Y, Piao S, Priyadarshi A, Lee EH, Kim HY, Jeon YH, Ha NC, Hwang KY Biochem Biophys Res Commun. 2010 Jan 1;391(1):990-4. Epub 2009 Dec 5. PMID:19968959^[1]

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

References

↑ Nam KH, Xu Y, Piao S, Priyadarshi A, Lee EH, Kim HY, Jeon YH, Ha NC, Hwang KY. Crystal structure of bacterioferritin from Rhodobacter sphaeroides. Biochem Biophys Res Commun. 2010 Jan 1;391(1):990-4. Epub 2009 Dec 5. PMID:19968959 doi:10.1016/j.bbrc.2009.12.003

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3gvy"

Categories: Cereibacter sphaeroides 2 4.1 | Large Structures | Hwang KY | Nam KH

@@ Line 1: / Line 1: @@
 ==Crystal structure of bacterioferritin from R.sphaeroides==
-<StructureSection load='3gvy' size='340' side='right' caption='[[3gvy]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='3gvy' size='340' side='right'caption='[[3gvy]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gvy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gvy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides_2.4.1 Cereibacter sphaeroides 2.4.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GVY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=3gvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gvy OCA], [http://pdbe.org/3gvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gvy RCSB], [http://www.ebi.ac.uk/pdbsum/3gvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gvy ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=3gvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gvy OCA], [https://pdbe.org/3gvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gvy RCSB], [https://www.ebi.ac.uk/pdbsum/3gvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gvy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q3J696_RHOS4 Q3J696_RHOS4]] Iron-storage protein (By similarity).[RuleBase:RU000623]  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 (By similarity).[PIRNR:PIRNR002560]
+[https://www.uniprot.org/uniprot/Q3J696_CERS4 Q3J696_CERS4] 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.[PIRNR:PIRNR002560]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gv/3gvy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gv/3gvy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 3gvy" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ferritin 3D structures|Ferritin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Rhodobacter sphaeroides]]
+[[Category: Cereibacter sphaeroides 2 4.1]]
-[[Category: Hwang, K Y]]
+[[Category: Large Structures]]
-[[Category: Nam, K H]]
+[[Category: Hwang KY]]
-[[Category: Bacterioferritin]]
+[[Category: Nam KH]]
-[[Category: Di-iron]]
-[[Category: Ferritin]]
-[[Category: Ferroxidase activity]]
-[[Category: Heme]]
-[[Category: Iron storage]]
-[[Category: Metal binding protein]]

3gvy

From Proteopedia

Current revision

Crystal structure of bacterioferritin from R.sphaeroides

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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