3ks0

From Proteopedia

(Difference between revisions)

Revision as of 20:20, 9 December 2016

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 Atcc 18824 and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1fcb, 1kbi
Gene:	CYB2, YML054C, YM9958.08C (ATCC 18824)
Activity:	L-lactate dehydrogenase (cytochrome), with EC number 1.1.2.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 Evolutionary Conservation
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/3ks0"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4==
 <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/Mus_musculus Mus musculus] and [http://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 [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 [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>
 </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>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fcb|1fcb]], [[1kbi|1kbi]]</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 Saccharomyces cerevisiae])</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='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://www.rcsb.org/pdb/explore.do?structureId=3ks0 RCSB], [http://www.ebi.ac.uk/pdbsum/3ks0 PDBsum]</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>
 == Evolutionary Conservation ==
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ks0 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ks0" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 37: @@
 __TOC__
 </StructureSection>
+[[Category: Atcc 18824]]
 [[Category: Mus musculus]]
-[[Category: Saccharomyces cerevisiae]]
 [[Category: Golinelli-Pimpaneau, B]]
 [[Category: Le, K H.D]]

3ks0

From Proteopedia

Revision as of 20:20, 9 December 2016

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

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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