2iv2: Difference between revisions

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[[Image:2iv2.gif|left|200px]]
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{{STRUCTURE_2iv2|  PDB=2iv2  |  SCENE=  }}
'''REINTERPRETATION OF REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI'''


==Reinterpretation of reduced form of formate dehydrogenase H from E. coli==
<StructureSection load='2iv2' size='340' side='right'caption='[[2iv2]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2iv2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IV2 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.27&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MD:GUANYLATE-O-PHOSPHORIC+ACID+MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)+ESTER'>2MD</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene></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=2iv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iv2 OCA], [https://pdbe.org/2iv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iv2 RCSB], [https://www.ebi.ac.uk/pdbsum/2iv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iv2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/FDHF_ECOLI FDHF_ECOLI] Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2iv2_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2iv2 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.


==Overview==
Formate-reduced E. coli formate dehydrogenase H: The reinterpretation of the crystal structure suggests a new reaction mechanism.,Raaijmakers HC, Romao MJ J Biol Inorg Chem. 2006 Oct;11(7):849-54. Epub 2006 Jul 8. PMID:16830149<ref>PMID:16830149</ref>
Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2IV2 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IV2 OCA].
</div>
<div class="pdbe-citations 2iv2" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Formate-reduced E. coli formate dehydrogenase H: The reinterpretation of the crystal structure suggests a new reaction mechanism., Raaijmakers HC, Romao MJ, J Biol Inorg Chem. 2006 Oct;11(7):849-54. Epub 2006 Jul 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16830149 16830149]
*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]]
[[Category: Formate dehydrogenase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Raaijmakers, H C.A.]]
__TOC__
[[Category: Romao, M J.]]
</StructureSection>
[[Category: 4fe-4]]
[[Category: Escherichia coli]]
[[Category: Anaerobic]]
[[Category: Large Structures]]
[[Category: Complete proteome]]
[[Category: Raaijmakers HCA]]
[[Category: Dehydrogenase]]
[[Category: Romao MJ]]
[[Category: Direct protein sequencing]]
[[Category: Fe4s4]]
[[Category: Formate]]
[[Category: Iron]]
[[Category: Iron sulfur cluster]]
[[Category: Iron-sulfur]]
[[Category: Metal-binding]]
[[Category: Mgd]]
[[Category: Molybdenum]]
[[Category: Molybdopterin]]
[[Category: Molybdopterin guanine dinucleotide]]
[[Category: Mpt]]
[[Category: Nad]]
[[Category: Oxidoreductase]]
[[Category: Secy]]
[[Category: Selenium]]
[[Category: Selenocysteine]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:55:27 2008''

Latest revision as of 17:22, 8 September 2026

Reinterpretation of reduced form of formate dehydrogenase H from E. coli

2iv2, resolution 2.27Å

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