1fdo: Difference between revisions

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[[Image:1fdo.jpg|left|200px]]


{{Structure
==OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI==
|PDB= 1fdo |SIZE=350|CAPTION= <scene name='initialview01'>1fdo</scene>, resolution 2.8&Aring;
<StructureSection load='1fdo' size='340' side='right'caption='[[1fdo]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE= <scene name='pdbsite=FS4:The+Fe+S+Cluster+Is+Coordinated+To+The+S+Atoms+Of+CYS+8,+...'>FS4</scene> and <scene name='pdbsite=MO4:The+Mo+Atom+Is+Coordinated+To+The+Se+Atom+Of+Sec+140,+Th+...'>MO4</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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> and <scene name='pdbligand=6MO:MOLYBDENUM(VI) ION'>6MO</scene>
<table><tr><td colspan='2'>[[1fdo]] 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=1FDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FDO FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE= FDHF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</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=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1fdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdo OCA], [https://pdbe.org/1fdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fdo RCSB], [https://www.ebi.ac.uk/pdbsum/1fdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fdo 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/fd/1fdo_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1fdo ConSurf].
<div style="clear:both"></div>


'''OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI'''
==See Also==
 
*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]]
 
*[[Non-Standard Residue|Non-Standard Residue]]
==Overview==
*[[Standard Residues|Standard Residues]]
Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.
__TOC__
 
</StructureSection>
==About this Structure==
1FDO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FDO OCA].
 
==Reference==
Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster., Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD, Science. 1997 Feb 28;275(5304):1305-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9036855 9036855]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Formate dehydrogenase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Boyington JC]]
[[Category: Boyington, J C.]]
[[Category: Sun PD]]
[[Category: Sun, P D.]]
[[Category: 6MO]]
[[Category: MGD]]
[[Category: SF4]]
[[Category: anaerobic]]
[[Category: dehydrogenase]]
[[Category: fe4s4]]
[[Category: formate]]
[[Category: iron sulfur cluster]]
[[Category: mgd]]
[[Category: molybdenum]]
[[Category: molybdopterin]]
[[Category: molybdopterin guanine dinucleotide]]
[[Category: mpt]]
[[Category: oxidoreductase]]
[[Category: secy]]
[[Category: selenium]]
[[Category: selenocysteine]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:07:45 2008''

Latest revision as of 10:13, 7 February 2024

OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLIOXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI

Structural highlights

1fdo is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FDHF_ECOLI Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1fdo, resolution 2.80Å

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