5jpr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:


==Neutron Structure of Compound II of Ascorbate Peroxidase==
==Neutron Structure of Compound II of Ascorbate Peroxidase==
<StructureSection load='5jpr' size='340' side='right' caption='[[5jpr]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
<StructureSection load='5jpr' size='340' side='right'caption='[[5jpr]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5jpr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JPR FirstGlance]. <br>
<table><tr><td colspan='2'>[[5jpr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JPR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.806&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=5jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpr OCA], [http://pdbe.org/5jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jpr RCSB], [http://www.ebi.ac.uk/pdbsum/5jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpr 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=5jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpr OCA], [https://pdbe.org/5jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jpr RCSB], [https://www.ebi.ac.uk/pdbsum/5jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpr ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q43758_SOYBN Q43758_SOYBN]
Catalytic heme enzymes carry out a wide range of oxidations in biology. They have in common a mechanism that requires formation of highly oxidized ferryl intermediates. It is these ferryl intermediates that provide the catalytic engine to drive the biological activity. Unravelling the nature of the ferryl species is of fundamental and widespread importance. The essential question is whether the ferryl is best described as a Fe(IV)=O or a Fe(IV)-OH species, but previous spectroscopic and X-ray crystallographic studies have not been able to unambiguously differentiate between the two species. Here we use a different approach. We report a neutron crystal structure of the ferryl intermediate in Compound II of a heme peroxidase; the structure allows the protonation states of the ferryl heme to be directly observed. This, together with pre-steady state kinetic analyses, electron paramagnetic resonance spectroscopy and single crystal X-ray fluorescence, identifies a Fe(IV)-OH species as the reactive intermediate. The structure establishes a precedent for the formation of Fe(IV)-OH in a peroxidase.


Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme.,Kwon H, Basran J, Casadei CM, Fielding AJ, Schrader TE, Ostermann A, Devos JM, Aller P, Blakeley MP, Moody PC, Raven EL Nat Commun. 2016 Nov 29;7:13445. doi: 10.1038/ncomms13445. PMID:27897163<ref>PMID:27897163</ref>
==See Also==
 
*[[Ascorbate peroxidase 3D structures|Ascorbate peroxidase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5jpr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: L-ascorbate peroxidase]]
[[Category: Glycine max]]
[[Category: Blakeley, M P]]
[[Category: Large Structures]]
[[Category: Kwon, H]]
[[Category: Blakeley MP]]
[[Category: Moody, P C.E]]
[[Category: Kwon H]]
[[Category: Raven, E L]]
[[Category: Moody PCE]]
[[Category: Compound ii]]
[[Category: Raven EL]]
[[Category: Cryo-trapping]]
[[Category: Ferryle heme]]
[[Category: Heme peroxidase]]
[[Category: Intermediate]]
[[Category: Oxidoreductase]]

Latest revision as of 10:24, 1 May 2024

Neutron Structure of Compound II of Ascorbate PeroxidaseNeutron Structure of Compound II of Ascorbate Peroxidase

Structural highlights

5jpr is a 1 chain structure with sequence from Glycine max. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Hybrid , Neutron Diffraction , X-ray diffraction, Resolution 1.806Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q43758_SOYBN

See Also

5jpr, resolution 1.81Å

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=5jpr&oldid=4137805"