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.

6y1t

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a Trp51 to S-Trp51 modification

Structural highlights

6y1t is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. 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.

Publication Abstract from PubMed

Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin pi-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase.,Ortmayer M, Hardy FJ, Quesne MG, Fisher K, Levy C, Heyes DJ, Catlow CRA, de Visser SP, Rigby SEJ, Hay S, Green AP JACS Au. 2021 Jul 26;1(7):913-918. doi: 10.1021/jacsau.1c00145. Epub 2021 May 14. PMID:34337604^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ortmayer M, Hardy FJ, Quesne MG, Fisher K, Levy C, Heyes DJ, Catlow CRA, de Visser SP, Rigby SEJ, Hay S, Green AP. A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase. JACS Au. 2021 Jul 26;1(7):913-918. doi: 10.1021/jacsau.1c00145. Epub 2021 May 14. PMID:34337604 doi:http://dx.doi.org/10.1021/jacsau.1c00145

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6y1t"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Green AP | Levy C | Ortmayer M

@@ Line 3: / Line 3: @@
 <StructureSection load='6y1t' size='340' side='right'caption='[[6y1t]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6y1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y1T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6y1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y1T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4OG:3-(1-BENZOTHIOPHEN-3-YL)-L-ALANINE'>4OG</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=4OG:3-(1-BENZOTHIOPHEN-3-YL)-L-ALANINE'>4OG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CCP1, CCP, CPO, YKR066C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=6y1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y1t OCA], [https://pdbe.org/6y1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y1t RCSB], [https://www.ebi.ac.uk/pdbsum/6y1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y1t 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.
+[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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
-[[Category: Cytochrome-c peroxidase]]
 [[Category: Large Structures]]
-[[Category: Green, A P]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Levy, C]]
+[[Category: Green AP]]
-[[Category: Ortmayer, M]]
+[[Category: Levy C]]
-[[Category: Engineered]]
+[[Category: Ortmayer M]]
-[[Category: Heme]]
-[[Category: Non-canonical amino acid]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxidase]]

6y1t

From Proteopedia

Current revision

The crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a Trp51 to S-Trp51 modification

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox