1dj5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:54, 7 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dj5.gif|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF R48A MUTANT OF CYTOCHROME C PEROXIDASE WITH N-HYDROXYGUANIDINE BOUND==
-
|PDB= 1dj5 |SIZE=350|CAPTION= <scene name='initialview01'>1dj5</scene>, resolution 1.93&Aring;
+
<StructureSection load='1dj5' size='340' side='right'caption='[[1dj5]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HGU:N-HYDROXYGUANIDINE'>HGU</scene>
+
<table><tr><td colspan='2'>[[1dj5]] 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=1DJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJ5 FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
-
|GENE=
+
<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=HGU:N-HYDROXYGUANIDINE'>HGU</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj5 OCA], [https://pdbe.org/1dj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1dj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dj5 ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1dj1|1DJ1]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj5 OCA], [http://www.ebi.ac.uk/pdbsum/1dj5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dj5 RCSB]</span>
+
== 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/dj/1dj5_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=1dj5 ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF R48A MUTANT OF CYTOCHROME C PEROXIDASE WITH N-HYDROXYGUANIDINE BOUND'''
+
==See Also==
-
 
+
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Heme enzymes are capable of catalyzing a range of oxidative chemistry with high specificity, depending on the surrounding protein environment. We describe here a reaction catalyzed by a mutant of cytochrome c peroxidase, which is similar but distinct from those catalyzed by nitric-oxide synthase. In the R48A mutant, an expanded water-filled cavity was created above the distal heme face. N-hydroxyguanidine (NHG) but not guanidine was shown to bind in the cavity with K(d) = 8.5 mM, and coordinate to the heme to give a low spin state. Reaction of R48A with peroxide produced a Fe(IV)=O/Trp(.+) center capable of oxidizing either NHG or N(omega)-hydroxyarginine (NHA), but not arginine or guanidine, by a multi-turnover catalytic process. Oxidation of either NHG or NHA by R48A did not result in the accumulation of NO, NO(2)(-), NO(3)(-), urea, or citrulline, but instead afforded a yellow product with absorption maxima of 257 and 400 nm. Mass spectrometry of the derivatized NHA products identified the yellow species as N-nitrosoarginine. We suggest that a nitrosylating agent, possibly derived from HNO, is produced by the oxidation of one molecule of substrate. This then reacts with a second substrate molecule to form the observed N-nitroso products. This complex chemistry illustrates how the active sites of enzymes such as nitric-oxide synthase may serve to prevent alternative reactions from occurring, in addition to enabling those desired.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1DJ5 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=1DJ5 OCA].
+
-
 
+
-
==Reference==
+
-
Unusual oxidative chemistry of N(omega)-hydroxyarginine and N-hydroxyguanidine catalyzed at an engineered cavity in a heme peroxidase., Hirst J, Goodin DB, J Biol Chem. 2000 Mar 24;275(12):8582-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10722697 10722697]
+
-
[[Category: Cytochrome-c peroxidase]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Goodin DB]]
-
[[Category: Goodin, D B.]]
+
[[Category: Hirst J]]
-
[[Category: Hirst, J.]]
+
-
[[Category: cavity mutant]]
+
-
[[Category: heme enzyme]]
+
-
[[Category: oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:42:28 2008''
+

Current revision

CRYSTAL STRUCTURE OF R48A MUTANT OF CYTOCHROME C PEROXIDASE WITH N-HYDROXYGUANIDINE BOUND

PDB ID 1dj5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dj5"
Personal tools