1jdr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1jdr.jpg|left|200px]]


{{Structure
==Crystal Structure of a Proximal Domain Potassium Binding Variant of Cytochrome c Peroxidase==
|PDB= 1jdr |SIZE=350|CAPTION= <scene name='initialview01'>1jdr</scene>, resolution 1.5&Aring;
<StructureSection load='1jdr' size='340' side='right'caption='[[1jdr]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
<table><tr><td colspan='2'>[[1jdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JDR FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
|GENE= OPBYC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=1jdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jdr OCA], [https://pdbe.org/1jdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jdr RCSB], [https://www.ebi.ac.uk/pdbsum/1jdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jdr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
== 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/jd/1jdr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1jdr ConSurf].
<div style="clear:both"></div>


'''Crystal Structure of a Proximal Domain Potassium Binding Variant of Cytochrome c Peroxidase'''
==See Also==
 
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Earlier work [Bonagura et al. (1996) Biochemistry 35, 6107] showed that the K+ site found in the proximal pocket of ascorbate peroxidase (APX) could be engineered into cytochrome c peroxidase (CCP). Binding of K+ at the engineered site results in a loss in activity and destabilization of the CCP compound I Trp191 cationic radical owing to long-range electrostatic effects. The engineered CCP mutant crystal structure has been refined to 1.5 A using data obtained at cryogenic temperatures which provides a more detailed basis for comparison with the naturally occurring K+ site in APX. The characteristic EPR signal associated with the Trp191 radical becomes progressively weaker as K+ is added, which correlates well with the loss in enzyme activity as [K+] is increased. These results coupled with stopped-flow studies support our earlier conclusions that the loss in activity and EPR signal is due to destabilization of the Trp191 cationic radical.
[[Category: Large Structures]]
 
==About this Structure==
1JDR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JDR OCA].
 
==Reference==
The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase., Bonagura CA, Sundaramoorthy M, Bhaskar B, Poulos TL, Biochemistry. 1999 Apr 27;38(17):5538-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10220341 10220341]
[[Category: Cytochrome-c peroxidase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Bhaskar B]]
[[Category: Bhaskar, B.]]
[[Category: Bonagura CA]]
[[Category: Bonagura, C A.]]
[[Category: Poulos TL]]
[[Category: Poulos, T L.]]
[[Category: Sundaramoorthy M]]
[[Category: Sundaramoorthy, M.]]
[[Category: HEM]]
[[Category: K]]
[[Category: helical bundle protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:02:04 2008''

Latest revision as of 10:38, 7 February 2024

Crystal Structure of a Proximal Domain Potassium Binding Variant of Cytochrome c PeroxidaseCrystal Structure of a Proximal Domain Potassium Binding Variant of Cytochrome c Peroxidase

Structural highlights

1jdr is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCPR_YEAST Destroys radicals which are normally produced within the cells and which are toxic to biological systems.

Evolutionary Conservation

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

See Also

1jdr, resolution 1.50Å

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=1jdr&oldid=4045236"