5mjc: Difference between revisions

Latest revision as of 18:45, 1 November 2023

metNeuroglobin under oxygen at 50 bar

Structural highlights

5mjc 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 1.62Å
Ligands:	DIO, HEM, OXY, SO4
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

A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.,Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prange T, Brunori M, Colloc'h N, Vallone B IUCrJ. 2019 Jul 10;6(Pt 5):832-842. doi: 10.1107/S2052252519008157. eCollection, 2019 Sep 1. PMID:31576217^[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:https://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:https://dx.doi.org/10.1074/jbc.M106438200
↑ Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prange T, Brunori M, Colloc'h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCrJ. 2019 Jul 10;6(Pt 5):832-842. doi: 10.1107/S2052252519008157. eCollection, 2019 Sep 1. PMID:31576217 doi:https://dx.doi.org/10.1107/S2052252519008157

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1074/jbc.M103907200

[2] 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:https://dx.doi.org/10.1074/jbc.M106438200

[3] Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prange T, Brunori M, Colloc'h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCrJ. 2019 Jul 10;6(Pt 5):832-842. doi: 10.1107/S2052252519008157. eCollection, 2019 Sep 1. PMID:31576217 doi:https://dx.doi.org/10.1107/S2052252519008157

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[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='5mjc' size='340' side='right'caption='[[5mjc]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mjc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MJC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MJC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mjc]] 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=5MJC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MJC 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=OXY:OXYGEN+MOLECULE'>OXY</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]] 1.62&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1oj6|1oj6]], [[3gkt|3gkt]], [[4o4t|4o4t]]</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=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ngb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5mjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mjc OCA], [https://pdbe.org/5mjc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mjc RCSB], [https://www.ebi.ac.uk/pdbsum/5mjc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mjc ProSAT]</span></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=5mjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mjc OCA], [http://pdbe.org/5mjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mjc RCSB], [http://www.ebi.ac.uk/pdbsum/5mjc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mjc 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 28: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Carpentier, P]]
+[[Category: Carpentier P]]
-[[Category: Prange, T]]
+[[Category: Colloc'h N]]
-[[Category: Vallone, B]]
+[[Category: Prange T]]
-[[Category: H, N Colloc]]
+[[Category: Vallone B]]
-[[Category: Oxygen complex storage cavity]]
-[[Category: Transport protein]]

5mjc: Difference between revisions

Latest revision as of 18:45, 1 November 2023

metNeuroglobin under oxygen at 50 bar

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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