This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1ryc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1ryc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ryc, resolution 1.8&Aring;" /> '''CYTOCHROME C PEROXIDA...)
Current revision (08:26, 14 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ryc.jpg|left|200px]]<br /><applet load="1ryc" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1ryc, resolution 1.8&Aring;" />
 
-
'''CYTOCHROME C PEROXIDASE W191G FROM SACCHAROMYCES CEREVISIAE'''<br />
 
-
==Overview==
+
==CYTOCHROME C PEROXIDASE W191G FROM SACCHAROMYCES CEREVISIAE==
-
Conformational changes that gate the access of substrates or ligands to an, active site are important features of enzyme function. In this report, we, describe an unusual example of a structural rearrangement near a buried, artificial cavity in cytochrome c peroxidase that occurs on binding, protonated benzimidazole. A hinged main-chain rotation at two residues, (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a, large solvent-accessible channel for the entry of ligands to an otherwise, inaccessible binding site. The trapping of this alternate conformational, state provides a unique view of the extent to which protein dynamics can, allow small molecule penetration into buried protein cavities.
+
<StructureSection load='1ryc' size='340' side='right'caption='[[1ryc]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1ryc]] 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=1RYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYC FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZI:BENZIMIDAZOLE'>BZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1ryc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryc OCA], [https://pdbe.org/1ryc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ryc RCSB], [https://www.ebi.ac.uk/pdbsum/1ryc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryc 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/ry/1ryc_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=1ryc ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1RYC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with HEM and BZI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RYC OCA].
+
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity., Fitzgerald MM, Musah RA, McRee DE, Goodin DB, Nat Struct Biol. 1996 Jul;3(7):626-31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8673607 8673607]
+
[[Category: Large Structures]]
-
[[Category: Cytochrome-c peroxidase]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Fitzgerald MM]]
-
[[Category: Fitzgerald, M.M.]]
+
[[Category: Goodin DB]]
-
[[Category: Goodin, D.B.]]
+
[[Category: Mcree DE]]
-
[[Category: Mcree, D.E.]]
+
[[Category: Musah R]]
-
[[Category: Musah, R.]]
+
-
[[Category: BZI]]
+
-
[[Category: HEM]]
+
-
[[Category: oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:57:25 2007''
+

Current revision

CYTOCHROME C PEROXIDASE W191G FROM SACCHAROMYCES CEREVISIAE

PDB ID 1ryc

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/1ryc"
Personal tools