2b0j: Difference between revisions

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<StructureSection load='2b0j' size='340' side='right'caption='[[2b0j]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='2b0j' size='340' side='right'caption='[[2b0j]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2b0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. 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>
<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>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </span></td></tr>
</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>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[[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).  
[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).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16540118<ref>PMID:16540118</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2b0j" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
[[Category: Atcc 43067]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ermler, U]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Hagemeier, C H]]
[[Category: Ermler U]]
[[Category: Mamat, B]]
[[Category: Hagemeier CH]]
[[Category: Pilak, O]]
[[Category: Mamat B]]
[[Category: Shima, S]]
[[Category: Pilak O]]
[[Category: Thauer, R K]]
[[Category: Shima S]]
[[Category: Vogt, S]]
[[Category: Thauer RK]]
[[Category: Vonrhein, C]]
[[Category: Vogt S]]
[[Category: Warkentin, E]]
[[Category: Vonrhein C]]
[[Category: Helix bundle]]
[[Category: Warkentin E]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold]]

Latest revision as of 13:42, 13 March 2024

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

2b0j, resolution 1.75Å

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