3fah

From Proteopedia

(Difference between revisions)

Current revision

Glycerol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas

Structural highlights

3fah is a 1 chain structure with sequence from Megalodesulfovibrio gigas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.72Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MOP_MEGGA

Evolutionary Conservation

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

Publication Abstract from PubMed

Aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is a member of the xanthine oxidase (XO) family of mononuclear Mo-enzymes that catalyzes the oxidation of aldehydes to carboxylic acids. The molybdenum site in the enzymes of the XO family shows a distorted square pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. We report here steady-state kinetic studies of DgAOR with the inhibitors cyanide, ethylene glycol, glycerol, and arsenite, together with crystallographic and EPR studies of the enzyme after reaction with the two alcohols. In contrast to what has been observed in other members of the XO family, cyanide, ethylene glycol, and glycerol are reversible inhibitors of DgAOR. Kinetic data with both cyanide and samples prepared from single crystals confirm that DgAOR does not need a sulfido ligand for catalysis and confirm the absence of this ligand in the coordination sphere of the molybdenum atom in the active enzyme. Addition of ethylene glycol and glycerol to dithionite-reduced DgAOR yields rhombic Mo(V) EPR signals, suggesting that the nearly square pyramidal coordination of the active enzyme is distorted upon alcohol inhibition. This is in agreement with the X-ray structure of the ethylene glycol and glycerol-inhibited enzyme, where the catalytically labile OH/OH(2) ligand is lost and both alcohols coordinate the Mo site in a eta(2) fashion. The two adducts present a direct interaction between the molybdenum and one of the carbon atoms of the alcohol moiety, which constitutes the first structural evidence for such a bond in a biological system.

Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system.,Santos-Silva T, Ferroni F, Thapper A, Marangon J, Gonzalez PJ, Rizzi AC, Moura I, Moura JJ, Romao MJ, Brondino CD J Am Chem Soc. 2009 Jun 17;131(23):7990-8. PMID:19459677^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Santos-Silva T, Ferroni F, Thapper A, Marangon J, Gonzalez PJ, Rizzi AC, Moura I, Moura JJ, Romao MJ, Brondino CD. Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system. J Am Chem Soc. 2009 Jun 17;131(23):7990-8. PMID:19459677 doi:10.1021/ja809448r

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fah"

Categories: Large Structures | Megalodesulfovibrio gigas | Romao MJ | Santos-Silva T

@@ Line 1: / Line 1: @@
 ==Glycerol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas==
-<StructureSection load='3fah' size='340' side='right' caption='[[3fah]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+<StructureSection load='3fah' size='340' side='right'caption='[[3fah]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fah]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FAH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FAH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fah]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FAH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FAH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene></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]] 1.72&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vlb|1vlb]], [[1sij|1sij]], [[1zcs|1zcs]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCD:(MOLYBDOPTERIN-CYTOSINE+DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)'>PCD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(FAD-independent) Aldehyde dehydrogenase (FAD-independent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.7 1.2.99.7] </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=3fah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fah OCA], [https://pdbe.org/3fah PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fah RCSB], [https://www.ebi.ac.uk/pdbsum/3fah PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fah ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fah OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fah RCSB], [http://www.ebi.ac.uk/pdbsum/3fah PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MOP_MEGGA MOP_MEGGA]
 == 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/fa/3fah_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/3fah_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/chain_selection.php?pdb_ID=2ata 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=3fah ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3fah" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio gigas]]
+[[Category: Large Structures]]
-[[Category: Romao, M J]]
+[[Category: Megalodesulfovibrio gigas]]
-[[Category: Santos-Silva, T]]
+[[Category: Romao MJ]]
-[[Category: Fad]]
+[[Category: Santos-Silva T]]
-[[Category: Flavoprotein]]
-[[Category: Iron]]
-[[Category: Iron-sulfur]]
-[[Category: Metal-binding]]
-[[Category: Mo-glycerol adduct]]
-[[Category: Molybdenum]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]

3fah

From Proteopedia

Current revision

Glycerol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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