2ghd: Difference between revisions

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<StructureSection load='2ghd' size='340' side='right'caption='[[2ghd]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='2ghd' size='340' side='right'caption='[[2ghd]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ghd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GHD FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ghd]] 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=2GHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GHD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ggn|2ggn]], [[2ghc|2ghc]], [[2ghe|2ghe]], [[2ghh|2ghh]], [[2ghk|2ghk]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ascorbate peroxidase ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </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=2ghd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ghd OCA], [https://pdbe.org/2ghd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ghd RCSB], [https://www.ebi.ac.uk/pdbsum/2ghd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ghd 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=2ghd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ghd OCA], [https://pdbe.org/2ghd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ghd RCSB], [https://www.ebi.ac.uk/pdbsum/2ghd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ghd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q43758_SOYBN Q43758_SOYBN]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ghd ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ghd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Conformational mobility of the distal histidine residue has been implicated for several different heme peroxidase enzymes, but unambiguous structural evidence is not available. In this work, we present mechanistic, spectroscopic, and structural evidence for peroxide- and ligand-induced conformational mobility of the distal histidine residue (His-42) in a site-directed variant of ascorbate peroxidase (W41A). In this variant, His-42 binds "on" to the heme in the oxidized form, duplicating the active site structure of the cytochromes b but, in contrast to the cytochromes b, is able to swing "off" the iron during catalysis. This conformational flexibility between the on and off forms is fully reversible and is used as a means to overcome the inherently unreactive nature of the on form toward peroxide, so that essentially complete catalytic activity is maintained. Contrary to the widely adopted view of heme enzyme catalysis, these data indicate that strong coordination of the distal histidine to the heme iron does not automatically undermine catalytic activity. The data add a new dimension to our wider appreciation of structure/activity correlations in other heme enzymes.
Conformational mobility in the active site of a heme peroxidase.,Badyal SK, Joyce MG, Sharp KH, Seward HE, Mewies M, Basran J, Macdonald IK, Moody PC, Raven EL J Biol Chem. 2006 Aug 25;281(34):24512-20. Epub 2006 Jun 7. PMID:16762924<ref>PMID:16762924</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ghd" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ascorbate peroxidase 3D structures|Ascorbate peroxidase 3D structures]]
*[[Ascorbate peroxidase 3D structures|Ascorbate peroxidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Glycine hispida]]
[[Category: Glycine max]]
[[Category: L-ascorbate peroxidase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Badyal, S K]]
[[Category: Badyal SK]]
[[Category: Joyce, M G]]
[[Category: Joyce MG]]
[[Category: Moody, P C.E]]
[[Category: Moody PCE]]
[[Category: Raven, E L]]
[[Category: Raven EL]]
[[Category: Sharp, K H]]
[[Category: Sharp KH]]
[[Category: Orthogonal bundle]]
[[Category: Oxidoreductase]]

Latest revision as of 12:27, 14 February 2024

Conformational mobility in the active site of a heme peroxidaseConformational mobility in the active site of a heme peroxidase

Structural highlights

2ghd 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:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q43758_SOYBN

Evolutionary Conservation

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

See Also

2ghd, resolution 1.40Å

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OCA
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