2d0v

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{{Seed}}
 
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[[Image:2d0v.png|left|200px]]
 
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==Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans==
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The line below this paragraph, containing "STRUCTURE_2d0v", creates the "Structure Box" on the page.
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<StructureSection load='2d0v' size='340' side='right'caption='[[2d0v]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2d0v]] is a 6 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=2D0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0V FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.49&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</scene></td></tr>
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{{STRUCTURE_2d0v| PDB=2d0v | SCENE= }}
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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=2d0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0v OCA], [https://pdbe.org/2d0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0v RCSB], [https://www.ebi.ac.uk/pdbsum/2d0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0v ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q4AE26_9HYPH Q4AE26_9HYPH]
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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/d0/2d0v_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=2d0v 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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===Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans===
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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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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 2d0v" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16533029}}, adds the Publication Abstract to the page
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*[[Methanol dehydrogenase|Methanol dehydrogenase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16533029 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16533029}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2D0V is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Hyphomicrobium_denitrificans Hyphomicrobium denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0V OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/16533029 16533029]
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[[Category: Hyphomicrobium denitrificans]]
[[Category: Hyphomicrobium denitrificans]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Hira, D.]]
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[[Category: Hira D]]
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[[Category: Nojiri, M.]]
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[[Category: Nojiri M]]
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[[Category: Suzuki, S.]]
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[[Category: Suzuki S]]
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[[Category: Yamaguchi, K.]]
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[[Category: Yamaguchi K]]
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[[Category: Calcium binding]]
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[[Category: Electron transfer]]
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[[Category: Methanol]]
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[[Category: Oxidoreductase]]
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[[Category: Pqq]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 20:40:04 2008''
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Current revision

Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans

PDB ID 2d0v

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