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1kol

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Crystal structure of formaldehyde dehydrogenase

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Retrieved from "http://52.214.119.220/wiki/index.php/1kol"

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-[[Image:1kol.gif|left|200px]]
- {{Structure
+==Crystal structure of formaldehyde dehydrogenase==
-|PDB= 1kol |SIZE=350|CAPTION= <scene name='initialview01'>1kol</scene>, resolution 1.65&Aring;
+<StructureSection load='1kol' size='340' side='right'caption='[[1kol]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1kol]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KOL FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Formaldehyde_dehydrogenase Formaldehyde dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.46 1.2.1.46] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kol OCA], [https://pdbe.org/1kol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kol RCSB], [https://www.ebi.ac.uk/pdbsum/1kol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kol ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kol OCA], [http://www.ebi.ac.uk/pdbsum/1kol PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kol RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/FADH_PSEPU FADH_PSEPU] Catalyzes the NAD(+)-dependent oxidation of formaldehyde and acetoaldehyde as well as long-chain alcohols but is inactive against propionaldehyde, butyraldehyde, methanol and ethanol. Can also catalyze the dismutation of a wide range of aldehydes such as formaldehyde.<ref>PMID:6526822</ref> <ref>PMID:9059646</ref>
+== Evolutionary Conservation ==
-'''Crystal structure of formaldehyde dehydrogenase'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/1kol_consurf.spt"</scriptWhenChecked>
-Formaldehyde dehydrogenase from Pseudomonas putida (PFDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family. The pyridine nucleotide NAD(H) in PFDH, which is distinct from the coenzyme (as cosubstrate) in typical alcohol dehydrogenases (ADHs), is tightly but not covalently bound to the protein and acts as a cofactor. PFDH can catalyze aldehyde dismutations without an external addition of NAD(H). The structural basis of the tightly bound cofactor of PFDH is unknown. The crystal structure of PFDH has been solved by the multiwavelength anomalous diffraction method using intrinsic zinc ions and has been refined at a 1.65 A resolution. The 170-kDa homotetrameric PFDH molecule shows 222 point group symmetry. Although the secondary structure arrangement and the binding mode of catalytic and structural zinc ions in PFDH are similar to those of typical ADHs, a number of loop structures that differ between PFDH and ADHs in their lengths and conformations are observed. A comparison of the present structure of PFDH with that of horse liver ADH, a typical example of an ADH, reveals that a long insertion loop of PFDH shields the adenine part of the bound NAD(+) molecule from the solvent, and a tight hydrogen bond network exists between the insertion loop and the adenine part of the cofactor, which is unique to PFDH. This insertion loop is conserved completely among the aldehyde-dismutating formaldehyde dehydrogenases, whereas it is replaced by a short turn among typical ADHs. Thus, the insertion loop specifically found among the aldehyde-dismutating formaldehyde dehydrogenases is responsible for the tight cofactor binding of these enzymes and explains why PFDH can effectively catalyze alternate oxidation and reduction of aldehydes without the release of cofactor molecule from the enzyme.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-KOL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KOL OCA].
+</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=1kol ConSurf].
+<div style="clear:both"></div>
-==Reference==
+== References ==
-Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases., Tanaka N, Kusakabe Y, Ito K, Yoshimoto T, Nakamura KT, J Mol Biol. 2002 Nov 29;324(3):519-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12445786 12445786]
+<references/>
-[[Category: Formaldehyde dehydrogenase]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Ito K]]
-[[Category: Ito, K.]]
+[[Category: Kusakabe Y]]
-[[Category: Kusakabe, Y.]]
+[[Category: Nakamura KT]]
-[[Category: Nakamura, K T.]]
+[[Category: Tanaka N]]
-[[Category: Tanaka, N.]]
+[[Category: Yoshimoto T]]
-[[Category: Yoshimoto, T.]]
-[[Category: dehydrogenase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:51:24 2008''

1kol

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Crystal structure of formaldehyde dehydrogenase

Structural highlights

Function

Evolutionary Conservation

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