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3f47

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{{Seed}}
 
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[[Image:3f47.png|left|200px]]
 
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==The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii==
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The line below this paragraph, containing "STRUCTURE_3f47", creates the "Structure Box" on the page.
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<StructureSection load='3f47' size='340' side='right'caption='[[3f47]], [[Resolution|resolution]] 1.75&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'>[[3f47]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. The March 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F47 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]] 1.75&#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=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=I2C:5-O-[(S)-HYDROXY{[2-HYDROXY-3,5-DIMETHYL-6-(2-OXOETHYL)PYRIDIN-4-YL]OXY}PHOSPHORYL]GUANOSINE'>I2C</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3f47| PDB=3f47 | 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=3f47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f47 OCA], [https://pdbe.org/3f47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f47 RCSB], [https://www.ebi.ac.uk/pdbsum/3f47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f47 ProSAT]</span></td></tr>
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</table>
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== Function ==
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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/f4/3f47_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=3f47 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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[Fe]-hydrogenase is one of three types of enzymes known to activate H(2). Crystal structure analysis recently revealed that its active site iron is ligated square-pyramidally by Cys176-sulfur, two CO, an "unknown" ligand and the sp(2)-hybridized nitrogen of a unique iron-guanylylpyridinol-cofactor. We report here on the structure of the C176A mutated enzyme crystallized in the presence of dithiothreitol (DTT). It suggests an iron center octahedrally coordinated by one DTT-sulfur and one DTT-oxygen, two CO, the 2-pyridinol's nitrogen and the 2-pyridinol's 6-formylmethyl group in an acyl-iron ligation. This result led to a re-interpretation of the iron ligation in the wild-type.
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===The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii===
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The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.,Hiromoto T, Ataka K, Pilak O, Vogt S, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Shima S, Ermler U FEBS Lett. 2009 Feb 4;583(3):585-90. Epub 2009 Jan 20. PMID:19162018<ref>PMID:19162018</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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The line below this paragraph, {{ABSTRACT_PUBMED_19162018}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3f47" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19162018 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19162018}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3F47 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. The March 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_03 10.2210/rcsb_pdb/mom_2009_03]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F47 OCA].
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==Reference==
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<ref group="xtra">PMID:19162018</ref><references group="xtra"/>
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[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
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[[Category: Hydrogenase]]
[[Category: Hydrogenase]]
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[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
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[[Category: Ermler, U.]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Hiromoto, T.]]
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[[Category: Ermler U]]
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[[Category: Pilak, O.]]
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[[Category: Hiromoto T]]
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[[Category: Shima, S.]]
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[[Category: Pilak O]]
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[[Category: Thauer, R K.]]
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[[Category: Shima S]]
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[[Category: Warkentin, E.]]
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[[Category: Thauer RK]]
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[[Category: Complex with iron guanylyl pyridinol cofactor]]
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[[Category: Warkentin E]]
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[[Category: Helix bundle]]
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[[Category: Methanogenesis]]
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[[Category: One-carbon metabolism]]
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[[Category: Oxidoreductase]]
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[[Category: Rossmann fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jun 2 12:44:45 2009''
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Current revision

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii

PDB ID 3f47

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