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.

5vrt

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Nonheme Iron Replacement in a Biosynthetic Nitric Oxide Reductase Model Performing O2 Reduction to Water: Co-bound FeBMb

Structural highlights

5vrt is a 1 chain structure with sequence from Physeter catodon. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.995Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYG_PHYMC Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Publication Abstract from PubMed

The presence of nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe and Co derivatives are similar, the percentage of reaction active species formation are 7%, 4% and 1% and the total turnovers are 5.1 +/- 1.1, 13.4 +/- 0.7, and 82.5 +/- 2.5, respectively. These results correlate with the trends of nonheme metal-binding dissociation constants (35 microM, 22 microM and 9 microM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions, and suggest that structural and electronic effects related to the presence of different nonheme metals lead to observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature's choice of metal ion, and reaction mechanism, and allows for finer control of the enzymatic activity, which is a basis for design of efficient catalysts for oxygen reduction reaction for fuel cells.

Manganese and Cobalt in the Nonheme Metal-binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-inactive Mechanism.,Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moenne-Loccoz P, Zhang Y, Lu Y J Am Chem Soc. 2017 Aug 3. doi: 10.1021/jacs.7b05800. PMID:28768416^[1]

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

References

↑ Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moenne-Loccoz P, Zhang Y, Lu Y. Manganese and Cobalt in the Nonheme Metal-binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-inactive Mechanism. J Am Chem Soc. 2017 Aug 3. doi: 10.1021/jacs.7b05800. PMID:28768416 doi:http://dx.doi.org/10.1021/jacs.7b05800

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/5vrt"

@@ Line 1: / Line 1: @@
 ==Nonheme Iron Replacement in a Biosynthetic Nitric Oxide Reductase Model Performing O2 Reduction to Water: Co-bound FeBMb==
-<StructureSection load='5vrt' size='340' side='right' caption='[[5vrt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5vrt' size='340' side='right'caption='[[5vrt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5vrt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VRT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5vrt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VRT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 1.995&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vrt OCA], [http://pdbe.org/5vrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vrt RCSB], [http://www.ebi.ac.uk/pdbsum/5vrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vrt ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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=5vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vrt OCA], [https://pdbe.org/5vrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vrt RCSB], [https://www.ebi.ac.uk/pdbsum/5vrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vrt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5vrt" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bhagi-Damodaran, A]]
+[[Category: Large Structures]]
-[[Category: Chakraborty, S]]
+[[Category: Physeter catodon]]
-[[Category: Lu, Y]]
+[[Category: Bhagi-Damodaran A]]
-[[Category: Mirs, E N]]
+[[Category: Chakraborty S]]
-[[Category: Moenne-Loccoz, P]]
+[[Category: Lu Y]]
-[[Category: Petrik, I D]]
+[[Category: Mirs EN]]
-[[Category: Reed, J]]
+[[Category: Moenne-Loccoz P]]
-[[Category: Ross, M]]
+[[Category: Petrik ID]]
-[[Category: Shi, Y]]
+[[Category: Reed J]]
-[[Category: Zhang, Y]]
+[[Category: Ross M]]
-[[Category: Zhu, Q]]
+[[Category: Shi Y]]
-[[Category: Biosynthetic]]
+[[Category: Zhang Y]]
-[[Category: Myoglobin]]
+[[Category: Zhu Q]]
-[[Category: Oxygen]]
-[[Category: Oxygen transport]]
-[[Category: Reduction]]

5vrt

From Proteopedia

Current revision

Nonheme Iron Replacement in a Biosynthetic Nitric Oxide Reductase Model Performing O2 Reduction to Water: Co-bound FeBMb

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