2ji3: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 3: Line 3:
<StructureSection load='2ji3' size='340' side='right'caption='[[2ji3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='2ji3' size='340' side='right'caption='[[2ji3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ji3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33931 Atcc 33931]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JI3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ji3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33931 Atcc 33931]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JI3 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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
</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>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vzg|1vzg]], [[1vzh|1vzh]], [[1vzi|1vzi]], [[2ji1|2ji1]], [[2ji2|2ji2]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vzg|1vzg]], [[1vzh|1vzh]], [[1vzi|1vzi]], [[2ji1|2ji1]], [[2ji2|2ji2]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dfx, rbo, Deba_2050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=453230 ATCC 33931])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dfx, rbo, Deba_2050 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=453230 ATCC 33931])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_reductase Superoxide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.2 1.15.1.2] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Superoxide_reductase Superoxide reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.2 1.15.1.2] </span></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=2ji3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji3 OCA], [http://pdbe.org/2ji3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ji3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ji3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji3 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=2ji3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji3 OCA], [https://pdbe.org/2ji3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ji3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ji3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DFX_DESB2 DFX_DESB2]] Catalyzes the one-electron reduction of superoxide anion radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a fundamental role in case of oxidative stress via its superoxide detoxification activity.<ref>PMID:10617593</ref>   
[[https://www.uniprot.org/uniprot/DFX_DESB2 DFX_DESB2]] Catalyzes the one-electron reduction of superoxide anion radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a fundamental role in case of oxidative stress via its superoxide detoxification activity.<ref>PMID:10617593</ref>   
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]

Revision as of 14:27, 31 March 2021

X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsiiX-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii

Structural highlights

2ji3 is a 4 chain structure with sequence from Atcc 33931. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Gene:dfx, rbo, Deba_2050 (ATCC 33931)
Activity:Superoxide reductase, with EC number 1.15.1.2
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DFX_DESB2] Catalyzes the one-electron reduction of superoxide anion radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a fundamental role in case of oxidative stress via its superoxide detoxification activity.[1]

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-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.

Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.,Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D Science. 2007 Apr 20;316(5823):449-53. PMID:17446401[2]

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

See Also

References

  1. ↑ Lombard M, Fontecave M, Touati D, Niviere V. Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. Evidence for a superoxide reductase activity. J Biol Chem. 2000 Jan 7;275(1):115-21. PMID:10617593
  2. ↑ Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D. Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme. Science. 2007 Apr 20;316(5823):449-53. PMID:17446401 doi:316/5823/449

2ji3, resolution 1.95Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2ji3&oldid=3377626"