1nf6

From Proteopedia

(Difference between revisions)

Current revision

X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)

Structural highlights

1nf6 is a 16 chain structure with sequence from Desulfovibrio desulfuricans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BFR_DESDA 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.

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

The first crystal structure of a native di-iron center in an iron-storage protein (bacterio)ferritin is reported. The protein, isolated from the anaerobic bacterium Desulfovibrio desulfuricans, has the unique property of having Fe-coproporphyrin III as its heme cofactor. The three-dimensional structure of this bacterioferritin was determined in three distinct catalytic/redox states by X-ray crystallography (at 1.95, 2.05 and 2.35 A resolution), corresponding to different intermediates of the di-iron ferroxidase site. Conformational changes associated with these intermediates support the idea of a route for iron entry into the protein shell through a pore that passes through the di-iron center. Molecular surface and electrostatic potential calculations also suggest the presence of another ion channel, distant from the channels at the three- and four-fold axes proposed as points of entry for the iron atoms.

The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans.,Macedo S, Romao CV, Mitchell E, Matias PM, Liu MY, Xavier AV, LeGall J, Teixeira M, Lindley P, Carrondo MA Nat Struct Biol. 2003 Apr;10(4):285-90. PMID:12627224^[1]

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

References

↑ Macedo S, Romao CV, Mitchell E, Matias PM, Liu MY, Xavier AV, LeGall J, Teixeira M, Lindley P, Carrondo MA. The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans. Nat Struct Biol. 2003 Apr;10(4):285-90. PMID:12627224 doi:10.1038/nsb909

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/1nf6"

@@ Line 3: / Line 3: @@
 <StructureSection load='1nf6' size='340' side='right'caption='[[1nf6]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nf6]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NF6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nf6]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NF6 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=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nf4|1nf4]], [[1nfv|1nfv]]</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=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1nf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf6 OCA], [http://pdbe.org/1nf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nf6 RCSB], [http://www.ebi.ac.uk/pdbsum/1nf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nf6 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=1nf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf6 OCA], [https://pdbe.org/1nf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nf6 RCSB], [https://www.ebi.ac.uk/pdbsum/1nf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nf6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BFR_DESDA BFR_DESDA]] 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.
+[https://www.uniprot.org/uniprot/BFR_DESDA BFR_DESDA] 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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nf/1nf6_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 38: / Line 38: @@
 [[Category: Desulfovibrio desulfuricans]]
 [[Category: Large Structures]]
-[[Category: Carrondo, M A]]
+[[Category: Carrondo MA]]
-[[Category: LeGall, J]]
+[[Category: LeGall J]]
-[[Category: Lindley, P]]
+[[Category: Lindley P]]
-[[Category: Liu, M Y]]
+[[Category: Liu MY]]
-[[Category: Macedo, S]]
+[[Category: Macedo S]]
-[[Category: Matias, P M]]
+[[Category: Matias PM]]
-[[Category: Mitchell, E]]
+[[Category: Mitchell E]]
-[[Category: Romao, C V]]
+[[Category: Romao CV]]
-[[Category: Teixeira, M]]
+[[Category: Teixeira M]]
-[[Category: Xavier, A V]]
+[[Category: Xavier AV]]
-[[Category: 24 subunits in the active molecule]]
-[[Category: Bacterioferritin]]
-[[Category: Diiron centre]]
-[[Category: Haem fe-coproporphyrin iii cofactor]]
-[[Category: Iron storage-electron transport complex]]

1nf6

From Proteopedia

Current revision

X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)

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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