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5o1k

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Crystal structure of murine neuroglobin mutant V140W under 20 bar xenon pressure

Structural highlights

5o1k is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NGB_MOUSE Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.^[1] ^[2]

Publication Abstract from PubMed

Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.

Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure.,Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prange T Biophys J. 2017 Nov 3. pii: S0006-3495(17)31129-3. doi:, 10.1016/j.bpj.2017.10.014. PMID:29108649^[3]

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

References

↑ Couture M, Burmester T, Hankeln T, Rousseau DL. The heme environment of mouse neuroglobin. Evidence for the presence of two conformations of the heme pocket. J Biol Chem. 2001 Sep 28;276(39):36377-82. Epub 2001 Jul 25. PMID:11473111 doi:http://dx.doi.org/10.1074/jbc.M103907200
↑ Dewilde S, Kiger L, Burmester T, Hankeln T, Baudin-Creuza V, Aerts T, Marden MC, Caubergs R, Moens L. Biochemical characterization and ligand binding properties of neuroglobin, a novel member of the globin family. J Biol Chem. 2001 Oct 19;276(42):38949-55. Epub 2001 Jul 25. PMID:11473128 doi:http://dx.doi.org/10.1074/jbc.M106438200
↑ Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prange T. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure. Biophys J. 2017 Nov 3. pii: S0006-3495(17)31129-3. doi:, 10.1016/j.bpj.2017.10.014. PMID:29108649 doi:http://dx.doi.org/10.1016/j.bpj.2017.10.014

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/5o1k"

Categories: Large Structures | Mus musculus | Colloc'h N | Prange T

@@ Line 1: / Line 1: @@
-==crystal structure of murine neuroglobin mutant V140W under 20 bar xenon pressure==
+==Crystal structure of murine neuroglobin mutant V140W under 20 bar xenon pressure==
-<StructureSection load='5o1k' size='340' side='right' caption='[[5o1k]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='5o1k' size='340' side='right'caption='[[5o1k]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5o1k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O1K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5o1k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O1K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 2.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5018|5018]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XE:XENON'>XE</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=5o1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o1k OCA], [http://pdbe.org/5o1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o1k RCSB], [http://www.ebi.ac.uk/pdbsum/5o1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o1k 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=5o1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o1k OCA], [https://pdbe.org/5o1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o1k RCSB], [https://www.ebi.ac.uk/pdbsum/5o1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o1k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NGB_MOUSE NGB_MOUSE]] Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.<ref>PMID:11473111</ref> <ref>PMID:11473128</ref>
+[https://www.uniprot.org/uniprot/NGB_MOUSE NGB_MOUSE] Involved in oxygen transport in the brain. Hexacoordinate globin, displaying competitive binding of oxygen or the distal His residue to the iron atom. Not capable of penetrating cell membranes. The deoxygenated form exhibits nitrite reductase activity inhibiting cellular respiration via NO-binding to cytochrome c oxidase. Involved in neuroprotection during oxidative stress. May exert its anti-apoptotic activity by acting to reset the trigger level of mitochondrial cytochrome c release necessary to commit the cells to apoptosis.<ref>PMID:11473111</ref> <ref>PMID:11473128</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5o1k" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Neuroglobin|Neuroglobin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: H, N COLLOC]]
+[[Category: Large Structures]]
-[[Category: PRANGE, T]]
+[[Category: Mus musculus]]
-[[Category: Globin]]
+[[Category: Colloc'h N]]
-[[Category: Oxygen transporter]]
+[[Category: Prange T]]
-[[Category: Transport protein]]

5o1k

From Proteopedia

Current revision

Crystal structure of murine neuroglobin mutant V140W under 20 bar xenon pressure

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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