2d0w

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(New page: 200px<br /><applet load="2d0w" size="350" color="white" frame="true" align="right" spinBox="true" caption="2d0w, resolution 1.98&Aring;" /> '''Crystal structure of...)
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[[Image:2d0w.gif|left|200px]]<br /><applet load="2d0w" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d0w, resolution 1.98&Aring;" />
 
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'''Crystal structure of cytochrome cL from Hyphomicrobium denitrificans'''<br />
 
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==Overview==
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==Crystal structure of cytochrome cL from Hyphomicrobium denitrificans==
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Methanol dehydrogenase (Hd-MDH) and its physiological electron acceptor, cytochrome c(L) (Hd-Cyt c(L)), isolated from a methylotrophic denitrifying, bacterium, Hyphomicrobium denitrificans A3151, have been kinetically and, structurally characterized; the X-ray structures of Hd-MDH and Hd-Cyt c(L), have been determined using molecular replacement at 2.5 and 2.0 A, resolution, respectively. To explain the mechanism for electron transfer, between these proteins, the dependence of MDH activity on the, concentration of Hd-Cyt c(L) has been investigated at pH 4.5-7.0. The, Michaelis constant for Hd-Cyt c(L) shows the smallest value (approximately, 0.3 microM) at pH 5.5. The pseudo-first-order rate constant (k(obs)) of, the reduction of Hd-Cyt c(L) exhibits a hyperbolic concentration, dependence of Hd-MDH at pH 5.5, although k(obs) linearly increases at pH, 6.5. These findings indicate formation of a transient complex between, these proteins during an electron transfer event. Hd-MDH (148 kDa) is a, large tetrameric protein with an alpha(2)beta(2) subunit composition, showing a high degree of structural similarity with other MDHs. Hd-Cyt, c(L) (19 kDa) exhibiting the alpha-band at 550.7 nm has a unique, C-terminal region involving a disulfide bond between Cys47 and Cys165., Moreover, there is a pair of Hd-Cyt c(L) monomers related with a, pseudo-2-fold axis of symmetry in the asymmetric unit, and the two, monomers tightly interact with each other through three hydrogen bonds., This configuration is the first example in the studies of cytochrome c as, the physiological electron acceptor for MDH. The docking simulation, between the coupled Hd-Cyt c(L) molecules and the heterotetrameric Hd-MDH, molecule has been carried out.
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<StructureSection load='2d0w' size='340' side='right'caption='[[2d0w]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d0w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyphomicrobium_denitrificans Hyphomicrobium denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0W FirstGlance]. <br>
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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]] 1.98&#8491;</td></tr>
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<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=ZN:ZINC+ION'>ZN</scene></td></tr>
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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=2d0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0w OCA], [https://pdbe.org/2d0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0w RCSB], [https://www.ebi.ac.uk/pdbsum/2d0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0w ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q4AE24_9HYPH Q4AE24_9HYPH] Electron acceptor for MDH. Acts in methanol oxidation.[PIRNR:PIRNR000008]
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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/d0/2d0w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d0w 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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Methanol dehydrogenase (Hd-MDH) and its physiological electron acceptor, cytochrome c(L) (Hd-Cyt c(L)), isolated from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans A3151, have been kinetically and structurally characterized; the X-ray structures of Hd-MDH and Hd-Cyt c(L) have been determined using molecular replacement at 2.5 and 2.0 A resolution, respectively. To explain the mechanism for electron transfer between these proteins, the dependence of MDH activity on the concentration of Hd-Cyt c(L) has been investigated at pH 4.5-7.0. The Michaelis constant for Hd-Cyt c(L) shows the smallest value (approximately 0.3 microM) at pH 5.5. The pseudo-first-order rate constant (k(obs)) of the reduction of Hd-Cyt c(L) exhibits a hyperbolic concentration dependence of Hd-MDH at pH 5.5, although k(obs) linearly increases at pH 6.5. These findings indicate formation of a transient complex between these proteins during an electron transfer event. Hd-MDH (148 kDa) is a large tetrameric protein with an alpha(2)beta(2) subunit composition, showing a high degree of structural similarity with other MDHs. Hd-Cyt c(L) (19 kDa) exhibiting the alpha-band at 550.7 nm has a unique C-terminal region involving a disulfide bond between Cys47 and Cys165. Moreover, there is a pair of Hd-Cyt c(L) monomers related with a pseudo-2-fold axis of symmetry in the asymmetric unit, and the two monomers tightly interact with each other through three hydrogen bonds. This configuration is the first example in the studies of cytochrome c as the physiological electron acceptor for MDH. The docking simulation between the coupled Hd-Cyt c(L) molecules and the heterotetrameric Hd-MDH molecule has been carried out.
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==About this Structure==
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Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins.,Nojiri M, Hira D, Yamaguchi K, Okajima T, Tanizawa K, Suzuki S Biochemistry. 2006 Mar 21;45(11):3481-92. PMID:16533029<ref>PMID:16533029</ref>
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2D0W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hyphomicrobium_denitrificans Hyphomicrobium denitrificans] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0W OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins., Nojiri M, Hira D, Yamaguchi K, Okajima T, Tanizawa K, Suzuki S, Biochemistry. 2006 Mar 21;45(11):3481-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16533029 16533029]
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</div>
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[[Category: Hyphomicrobium denitrificans]]
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<div class="pdbe-citations 2d0w" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Hira, D.]]
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[[Category: Nojiri, M.]]
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[[Category: Suzuki, S.]]
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[[Category: Yamaguchi, K.]]
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[[Category: HEM]]
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[[Category: ZN]]
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[[Category: cytochrome]]
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[[Category: electron transfer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:52:35 2008''
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==See Also==
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Hyphomicrobium denitrificans]]
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[[Category: Large Structures]]
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[[Category: Hira D]]
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[[Category: Nojiri M]]
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[[Category: Suzuki S]]
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[[Category: Yamaguchi K]]

Current revision

Crystal structure of cytochrome cL from Hyphomicrobium denitrificans

PDB ID 2d0w

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