1kbi

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[[Image:1kbi.gif|left|200px]]
 
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{{Structure
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==Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme==
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|PDB= 1kbi |SIZE=350|CAPTION= <scene name='initialview01'>1kbi</scene>, resolution 2.3&Aring;
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<StructureSection load='1kbi' size='340' side='right'caption='[[1kbi]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>
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<table><tr><td colspan='2'>[[1kbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBI FirstGlance]. <br>
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|ACTIVITY= <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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbi OCA], [https://pdbe.org/1kbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbi RCSB], [https://www.ebi.ac.uk/pdbsum/1kbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbi ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1fcb|1FCB]], [[1kbj|1KBJ]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbi OCA], [http://www.ebi.ac.uk/pdbsum/1kbi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kbi RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/CYB2_YEAST CYB2_YEAST]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kbi_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1kbi ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Flavocytochrome b(2) catalyzes the oxidation of L-lactate to pyruvate and the transfer of electrons to cytochrome c. The enzyme consists of a flavin-binding domain, which includes the active site for lacate oxidation, and a b(2)-cytochrome domain, required for efficient cytochrome c reduction. To better understand the structure and function of intra- and interprotein electron transfer, we have determined the crystal structure of the independently expressed flavin-binding domain of flavocytochrome b(2) to 2.50 A resolution and compared this with the structure of the intact enzyme, redetermined at 2.30 A resolution, both structures being from crystals cooled to 100 K. Whereas there is little overall difference between these structures, we do observe significant local changes near the interface region, some of which impact on amino acid side chains, such as Arg289, that have been shown previously to have an important role in catalysis. The disordered loop region found in flavocytochrome b(2) and its close homologues remain unresolved in frozen crystals of the flavin-binding domain, implying that the presence of the b(2)-cytochrome domain is not responsible for this positional disorder. The flavin-binding domain interacts poorly with cytochrome c, but we have introduced acidic residues in the interdomain interface region with the aim of enhancing cytochrome c binding. While the mutations L199E and K201E within the flavin-binding domain resulted in unimpaired lactate dehydrogenase activity, they failed to enhance electron-transfer rates with cytochrome c. This is most likely due to the disordered loop region obscuring all or part of the surface having the potential for productive interaction with cytochrome c.
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'''Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme'''
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Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme.,Cunane LM, Barton JD, Chen ZW, Welsh FE, Chapman SK, Reid GA, Mathews FS Biochemistry. 2002 Apr 2;41(13):4264-72. PMID:11914072<ref>PMID:11914072</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1kbi" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Flavocytochrome b(2) catalyzes the oxidation of L-lactate to pyruvate and the transfer of electrons to cytochrome c. The enzyme consists of a flavin-binding domain, which includes the active site for lacate oxidation, and a b(2)-cytochrome domain, required for efficient cytochrome c reduction. To better understand the structure and function of intra- and interprotein electron transfer, we have determined the crystal structure of the independently expressed flavin-binding domain of flavocytochrome b(2) to 2.50 A resolution and compared this with the structure of the intact enzyme, redetermined at 2.30 A resolution, both structures being from crystals cooled to 100 K. Whereas there is little overall difference between these structures, we do observe significant local changes near the interface region, some of which impact on amino acid side chains, such as Arg289, that have been shown previously to have an important role in catalysis. The disordered loop region found in flavocytochrome b(2) and its close homologues remain unresolved in frozen crystals of the flavin-binding domain, implying that the presence of the b(2)-cytochrome domain is not responsible for this positional disorder. The flavin-binding domain interacts poorly with cytochrome c, but we have introduced acidic residues in the interdomain interface region with the aim of enhancing cytochrome c binding. While the mutations L199E and K201E within the flavin-binding domain resulted in unimpaired lactate dehydrogenase activity, they failed to enhance electron-transfer rates with cytochrome c. This is most likely due to the disordered loop region obscuring all or part of the surface having the potential for productive interaction with cytochrome c.
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*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1KBI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBI OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme., Cunane LM, Barton JD, Chen ZW, Welsh FE, Chapman SK, Reid GA, Mathews FS, Biochemistry. 2002 Apr 2;41(13):4264-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11914072 11914072]
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[[Category: L-lactate dehydrogenase (cytochrome)]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Barton JD]]
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[[Category: Barton, J D.]]
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[[Category: Chapman SK]]
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[[Category: Chapman, S K.]]
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[[Category: Chen Z-W]]
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[[Category: Chen, Z W.]]
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[[Category: Cunane LM]]
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[[Category: Cunane, L M.]]
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[[Category: Mathews FS]]
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[[Category: Mathews, F S.]]
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[[Category: Reid GA]]
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[[Category: Reid, G A.]]
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[[Category: Welsh FE]]
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[[Category: Welsh, F E.]]
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[[Category: electron transfer]]
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[[Category: flavocytochrome b2]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:46:08 2008''
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Current revision

Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme

PDB ID 1kbi

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