5eqm

From Proteopedia

(Difference between revisions)

Revision as of 10:38, 28 July 2021

Crystal structure of murine neuroglobin at 310 MPa pressure

Structural highlights

5eqm is a 1 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	5eet, 5eoh
Gene:	Ngb (LK3 transgenic mice)
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

Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the "heme sliding mechanism". Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.

Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.,Colloc'h N, Sacquin-Mora S, Avella G, Dhaussy AC, Prange T, Vallone B, Girard E Sci Rep. 2017 May 12;7(1):1858. doi: 10.1038/s41598-017-02097-1. PMID:28500341^[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, Sacquin-Mora S, Avella G, Dhaussy AC, Prange T, Vallone B, Girard E. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep. 2017 May 12;7(1):1858. doi: 10.1038/s41598-017-02097-1. PMID:28500341 doi:http://dx.doi.org/10.1038/s41598-017-02097-1

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/5eqm"

@@ Line 3: / Line 3: @@
 <StructureSection load='5eqm' size='340' side='right'caption='[[5eqm]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5eqm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EQM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EQM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5eqm]] is a 1 chain structure with sequence from [https://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=5EQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EQM FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5eet|5eet]], [[5eoh|5eoh]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5eet|5eet]], [[5eoh|5eoh]]</div></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5eqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eqm OCA], [http://pdbe.org/5eqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eqm RCSB], [http://www.ebi.ac.uk/pdbsum/5eqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eqm ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ngb ([https://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=5eqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eqm OCA], [https://pdbe.org/5eqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eqm RCSB], [https://www.ebi.ac.uk/pdbsum/5eqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eqm 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 27: / Line 28: @@
 </StructureSection>
 [[Category: Large Structures]]
+[[Category: Lk3 transgenic mice]]
 [[Category: Girard, E]]
 [[Category: Prange, T]]
@@ Line 32: / Line 34: @@
 [[Category: H, N Colloc]]
 [[Category: Globin]]
+[[Category: Hpmx]]
 [[Category: Oxygen storage-transporter]]
 [[Category: Transport protein]]

5eqm

From Proteopedia

Revision as of 10:38, 28 July 2021

Crystal structure of murine neuroglobin at 310 MPa pressure

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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