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6cf0

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Sperm Whale Myoglobin H64V Mutant with Nitrite

Structural highlights

6cf0 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 1.64Å
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 globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb(III) and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb(III) and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb(II)-mediated reductions of nitrite to NO and structural data for the wt and mutant Mb(II)-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.,Wang B, Shi Y, Tejero J, Powell SM, Thomas LM, Gladwin MT, Shiva S, Zhang Y, Richter-Addo GB Biochemistry. 2018 Aug 14;57(32):4788-4802. doi: 10.1021/acs.biochem.8b00542., Epub 2018 Jul 27. PMID:29999305^[1]

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

References

↑ Wang B, Shi Y, Tejero J, Powell SM, Thomas LM, Gladwin MT, Shiva S, Zhang Y, Richter-Addo GB. Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry. 2018 Aug 14;57(32):4788-4802. doi: 10.1021/acs.biochem.8b00542., Epub 2018 Jul 27. PMID:29999305 doi:http://dx.doi.org/10.1021/acs.biochem.8b00542

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/6cf0"

@@ Line 3: / Line 3: @@
 <StructureSection load='6cf0' size='340' side='right'caption='[[6cf0]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6cf0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phymc Phymc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CF0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CF0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6cf0]] 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=6CF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CF0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.64&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 PHYMC])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6cf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cf0 OCA], [http://pdbe.org/6cf0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cf0 RCSB], [http://www.ebi.ac.uk/pdbsum/6cf0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cf0 ProSAT]</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=6cf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cf0 OCA], [https://pdbe.org/6cf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cf0 RCSB], [https://www.ebi.ac.uk/pdbsum/6cf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cf0 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 27: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Phymc]]
+[[Category: Physeter catodon]]
-[[Category: Powell, S M]]
+[[Category: Powell SM]]
-[[Category: Richter-Addo, G B]]
+[[Category: Richter-Addo GB]]
-[[Category: Thomas, L M]]
+[[Category: Thomas LM]]
-[[Category: Wang, B]]
+[[Category: Wang B]]
-[[Category: Myoglobin]]
-[[Category: Nitrite]]
-[[Category: Oxygen storage]]
-[[Category: Sperm whale]]

6cf0

From Proteopedia

Current revision

Sperm Whale Myoglobin H64V Mutant with Nitrite

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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