3lf5

From Proteopedia

(Difference between revisions)

Current revision

Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution

Structural highlights

3lf5 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.25Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NB5R4_HUMAN NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

NADH cytochrome b(5) oxidoreductase (Ncb5or) is found in animals and contains three domains similar to cytochrome b(5) (b(5)), CHORD-SGT1 (CS), and cytochrome b(5) reductase (b(5)R). Ncb5or has an important function, as suggested by the diabetes and lipoatrophy phenotypes in Ncb5or null mice. To elucidate the structural and functional properties of human Ncb5or, we generated its individual b(5) and b(5)R domains (Ncb5or-b(5) and Ncb5or-b(5)R, respectively) and compared them with human microsomal b(5) (Cyb5A) and b(5)R (Cyb5R3). A 1.25 A x-ray crystal structure of Ncb5or-b(5) reveals nearly orthogonal planes of the imidazolyl rings of heme-ligating residues His(89) and His(112), consistent with a highly anisotropic low spin EPR spectrum. Ncb5or is the first member of the cytochrome b(5) family shown to have such a heme environment. Like other b(5) family members, Ncb5or-b(5) has two helix-loop-helix motifs surrounding heme. However, Ncb5or-b(5) differs from Cyb5A with respect to location of the second heme ligand (His(112)) and of polypeptide conformation in its vicinity. Electron transfer from Ncb5or-b(5)R to Ncb5or-b(5) is much less efficient than from Cyb5R3 to Cyb5A, possibly as a consequence of weaker electrostatic interactions. The CS linkage probably obviates the need for strong interactions between b(5) and b(5)R domains in Ncb5or. Studies with a construct combining the Ncb5or CS and b(5)R domains suggest that the CS domain facilitates docking of the b(5) and b(5)R domains. Trp(114) is an invariant surface residue in all known Ncb5or orthologs but appears not to contribute to electron transfer from the b(5)R domain to the b(5) domain.

Study of the individual cytochrome b5 and cytochrome b5 reductase domains of Ncb5or reveals a unique heme pocket and a possible role of the CS domain.,Deng B, Parthasarathy S, Wang W, Gibney BR, Battaile KP, Lovell S, Benson DR, Zhu H J Biol Chem. 2010 Sep 24;285(39):30181-91. Epub 2010 Jul 14. PMID:20630863^[1]

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

References

↑ Deng B, Parthasarathy S, Wang W, Gibney BR, Battaile KP, Lovell S, Benson DR, Zhu H. Study of the individual cytochrome b5 and cytochrome b5 reductase domains of Ncb5or reveals a unique heme pocket and a possible role of the CS domain. J Biol Chem. 2010 Sep 24;285(39):30181-91. Epub 2010 Jul 14. PMID:20630863 doi:http://dx.doi.org/10.1074/jbc.M110.120329

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lf5"

@@ Line 1: / Line 1: @@
 ==Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution==
-<StructureSection load='3lf5' size='340' side='right' caption='[[3lf5]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
+<StructureSection load='3lf5' size='340' side='right'caption='[[3lf5]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lf5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lf5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LF5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.25&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-b5_reductase Cytochrome-b5 reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.2.2 1.6.2.2] </span></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='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=3lf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lf5 OCA], [http://pdbe.org/3lf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lf5 RCSB], [http://www.ebi.ac.uk/pdbsum/3lf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lf5 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=3lf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lf5 OCA], [https://pdbe.org/3lf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lf5 RCSB], [https://www.ebi.ac.uk/pdbsum/3lf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lf5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NB5R4_HUMAN NB5R4_HUMAN]] NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.
+[https://www.uniprot.org/uniprot/NB5R4_HUMAN NB5R4_HUMAN] NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lf/3lf5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lf/3lf5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Cytochrome-b5 reductase]]
+[[Category: Homo sapiens]]
-[[Category: Battaile, K P]]
+[[Category: Large Structures]]
-[[Category: Benson, D R]]
+[[Category: Battaile KP]]
-[[Category: Deng, B]]
+[[Category: Benson DR]]
-[[Category: Gibney, B R]]
+[[Category: Deng B]]
-[[Category: Lovell, S]]
+[[Category: Gibney BR]]
-[[Category: Parthasarathy, S]]
+[[Category: Lovell S]]
-[[Category: Wang, W]]
+[[Category: Parthasarathy S]]
-[[Category: Zhu, H]]
+[[Category: Wang W]]
-[[Category: Electron transfer]]
+[[Category: Zhu H]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Nad]]
-[[Category: Ncb5or]]
-[[Category: Oxidoreductase]]
-[[Category: Redox]]

3lf5

From Proteopedia

Current revision

Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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