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2b0j

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(New page: 200px<br /><applet load="2b0j" size="450" color="white" frame="true" align="right" spinBox="true" caption="2b0j, resolution 1.75&Aring;" /> '''The crystal structur...)
Current revision (13:42, 13 March 2024) (edit) (undo)
 
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[[Image:2b0j.gif|left|200px]]<br /><applet load="2b0j" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2b0j, resolution 1.75&Aring;" />
 
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'''The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)'''<br />
 
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==Overview==
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==The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)==
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The iron-sulphur cluster-free hydrogenase (Hmd, EC 1.12.98.2) from, methanogenic archaea is a novel type of hydrogenase that tightly binds an, iron-containing cofactor. The iron is coordinated by two CO molecules, one, sulphur and a pyridone derivative, which is linked via a phosphodiester, bond to a guanosine base. We report here on the crystal structure of the, Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 A and from, Methanopyrus kandleri at 2.4 A resolution. Homodimeric Hmd reveals a, unique architecture composed of one central and two identical peripheral, globular units. The central unit is composed of the intertwined C-terminal, segments of both subunits, forming a novel intersubunit fold. The two, peripheral units consist of the N-terminal domain of each subunit. The, Rossmann fold-like structure of the N-terminal domain contains a, mononucleotide-binding site, which could harbour the GMP moiety of the, cofactor. Another binding site for the iron-containing cofactor is most, probably Cys176, which is located at the bottom of a deep intersubunit, cleft and which has been shown to be essential for enzyme activity., Adjacent to the iron of the cofactor modelled as a ligand to Cys176, an, extended U-shaped extra electron density, interpreted as a, polyethyleneglycol fragment, suggests a binding site for the substrate, methenyltetrahydromethanopterin.
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<StructureSection load='2b0j' size='340' side='right'caption='[[2b0j]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2b0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B0J FirstGlance]. <br>
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2B0J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Active as [http://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2B0J OCA].
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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]] 1.75&#8491;</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=2b0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b0j OCA], [https://pdbe.org/2b0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b0j RCSB], [https://www.ebi.ac.uk/pdbsum/2b0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b0j ProSAT]</span></td></tr>
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==Reference==
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</table>
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The crystal structure of the apoenzyme of the iron-sulphur cluster-free hydrogenase., Pilak O, Mamat B, Vogt S, Hagemeier CH, Thauer RK, Shima S, Vonrhein C, Warkentin E, Ermler U, J Mol Biol. 2006 May 5;358(3):798-809. Epub 2006 Mar 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16540118 16540118]
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== Function ==
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[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
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[https://www.uniprot.org/uniprot/HMD_METJA HMD_METJA] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT (By similarity).
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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/b0/2b0j_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=2b0j ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
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[[Category: Single protein]]
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[[Category: Ermler U]]
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[[Category: Ermler, U.]]
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[[Category: Hagemeier CH]]
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[[Category: Hagemeier, C.H.]]
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[[Category: Mamat B]]
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[[Category: Mamat, B.]]
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[[Category: Pilak O]]
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[[Category: Pilak, O.]]
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[[Category: Shima S]]
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[[Category: Shima, S.]]
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[[Category: Thauer RK]]
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[[Category: Thauer, R.K.]]
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[[Category: Vogt S]]
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[[Category: Vogt, S.]]
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[[Category: Vonrhein C]]
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[[Category: Vonrhein, C.]]
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[[Category: Warkentin E]]
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[[Category: Warkentin, E.]]
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[[Category: helix bundle]]
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[[Category: rossmann fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:30:07 2007''
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Current revision

The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)

PDB ID 2b0j

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