2b0j: Difference between revisions

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[[Image:2b0j.gif|left|200px]]


<!--
==The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)==
The line below this paragraph, containing "STRUCTURE_2b0j", creates the "Structure Box" on the page.
<StructureSection load='2b0j' size='340' side='right'caption='[[2b0j]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_2b0j|  PDB=2b0j  |  SCENE= }}
</table>
 
== Function ==
'''The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)'''
[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 ==
 
[[Image:Consurf_key_small.gif|200px|right]]
==Overview==
Check<jmol>
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.
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b0/2b0j_consurf.spt"</scriptWhenChecked>
==About this Structure==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
2B0J is a [[Single protein]] structure of sequence from [http://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].  
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==Reference==
</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].
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://www.ncbi.nlm.nih.gov/pubmed/16540118 16540118]
<div style="clear:both"></div>
[[Category: 5,10-methenyltetrahydromethanopterin hydrogenase]]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Single protein]]
[[Category: Ermler U]]
[[Category: Ermler, U.]]
[[Category: Hagemeier CH]]
[[Category: Hagemeier, C H.]]
[[Category: Mamat B]]
[[Category: Mamat, B.]]
[[Category: Pilak O]]
[[Category: Pilak, O.]]
[[Category: Shima S]]
[[Category: Shima, S.]]
[[Category: Thauer RK]]
[[Category: Thauer, R K.]]
[[Category: Vogt S]]
[[Category: Vogt, S.]]
[[Category: Vonrhein C]]
[[Category: Vonrhein, C.]]
[[Category: Warkentin E]]
[[Category: Warkentin, E.]]
[[Category: Helix bundle]]
[[Category: Rossmann fold]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:42:05 2008''

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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