3ks0

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4

Structural highlights

3ks0 is a 6 chain structure with sequence from Mus musculus and Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CYB2_YEAST

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

Yeast flavocytochrome b(2) (Fcb2) is an L-lactate:cytochrome c oxidoreductase in the mitochondrial intermembrane space participating in cellular respiration. Each enzyme subunit consists of a cytochrome b(5)-like heme domain and a flavodehydrogenase (FDH) domain. In the Fcb2 crystal structure, the heme domain is mobile relative to the tetrameric FDH core in one out of two subunits. The monoclonal antibody B2B4, elicited against the holoenzyme, recognizes only the native heme domain in the holoenzyme. When bound, it suppresses the intramolecular electron transfer from flavin to heme b(2), hence cytochrome c reduction. We report here the crystal structure of the heme domain in complex with the Fab at 2.7 A resolution. The Fab epitope on the heme domain includes the two exposed propionate groups of the heme, which are hidden in the interface between the domains in the complete subunit. The structure discloses an unexpected plasticity of Fcb2 in the neighborhood of the heme cavity, in which the heme has rotated. The epitope overlaps with the docking area of the FDH domain onto the heme domain, indicating that the antibody displaces the heme domain in a movement of large amplitude. We suggest that the binding sites on the heme domain of cytochrome c and of the FDH domain also overlap and therefore that cytochrome c binding also requires the heme domain to move away from the FDH domain, so as to allow electron transfer between the two hemes. Based on this hypothesis, we propose a possible model of the Fcb2.cytochrome c complex. Interestingly, this model shares similarity with that of the cytochrome b(5) x cytochrome c complex, in which cytochrome c binds to the surface around the exposed heme edge of cytochrome b(5). The present results therefore support the idea that the heme domain mobility is an inherent component of the Fcb2 functioning.

Structural evidence for the functional importance of the heme domain mobility in flavocytochrome b2.,Diep Le KH, Lederer F, Golinelli-Pimpaneau B J Mol Biol. 2010 Jul 16;400(3):518-30. Epub 2010 May 28. PMID:20546754^[1]

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

References

↑ Diep Le KH, Lederer F, Golinelli-Pimpaneau B. Structural evidence for the functional importance of the heme domain mobility in flavocytochrome b2. J Mol Biol. 2010 Jul 16;400(3):518-30. Epub 2010 May 28. PMID:20546754 doi:10.1016/j.jmb.2010.05.035

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ks0"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ks0' size='340' side='right'caption='[[3ks0]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ks0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KS0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KS0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ks0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KS0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KS0 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></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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fcb|1fcb]], [[1kbi|1kbi]]</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></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYB2, YML054C, YM9958.08C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3ks0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ks0 OCA], [https://pdbe.org/3ks0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ks0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ks0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ks0 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=3ks0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ks0 OCA], [http://pdbe.org/3ks0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ks0 RCSB], [http://www.ebi.ac.uk/pdbsum/3ks0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ks0 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYB2_YEAST CYB2_YEAST]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ks/3ks0_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Lactate Dehydrogenase|Lactate Dehydrogenase]]
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Golinelli-Pimpaneau, B]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Le, K H.D]]
+[[Category: Golinelli-Pimpaneau B]]
-[[Category: Lederer, F]]
+[[Category: Le KHD]]
-[[Category: Antibody]]
+[[Category: Lederer F]]
-[[Category: Domain mobility]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]
-[[Category: Epitope]]
-[[Category: Fab]]
-[[Category: Flavocytochrome b2]]
-[[Category: Flavoprotein]]
-[[Category: Fmn]]
-[[Category: Heme]]
-[[Category: Heme domain]]
-[[Category: Metal-binding]]
-[[Category: Mitochondrion]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]
-[[Category: Transit peptide]]
-[[Category: Transport]]

3ks0

From Proteopedia

Current revision

Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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