3afn: Difference between revisions

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-{{Seed}}
-[[Image:3afn.png|left|200px]]
-<!--
+==Crystal structure of aldose reductase A1-R complexed with NADP==
-The line below this paragraph, containing "STRUCTURE_3afn", creates the "Structure Box" on the page.
+<StructureSection load='3afn' size='340' side='right'caption='[[3afn]], [[Resolution|resolution]] 1.63&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'>[[3afn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AFN 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]] 1.63&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=TBU:TERTIARY-BUTYL+ALCOHOL'>TBU</scene></td></tr>
-{{STRUCTURE_3afn|  PDB=3afn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3afn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afn OCA], [https://pdbe.org/3afn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3afn RCSB], [https://www.ebi.ac.uk/pdbsum/3afn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3afn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/D6RU56_9SPHN D6RU56_9SPHN]
+== 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/af/3afn_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=3afn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In Sphingomonas sp. A1, alginate is degraded by alginate lyases to its constituent monosaccharides, which are nonenzymatically converted to an alpha-keto acid, namely, 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH). The properties of the DEH-metabolizing enzyme and its gene in strain A1 were characterized. In the presence of alginate, strain A1 cells inducibly produced an NADPH-dependent DEH reductase (A1-R) in their cytoplasm. Molecular cloning of the enzyme gene indicated that A1-R belonged to the short-chain dehydrogenase/reductase superfamily and catalyzed the conversion of DEH to 2-keto-3-deoxy-d-gluconic acid most efficiently at around pH 7.0 and 50 masculineC. Crystal structures of A1-R and its complex with NADP were determined at around 1.6A resolution by X-ray crystallography. The enzyme consists of three layers (alpha/beta/alpha), with a coenzyme-binding Rossmann fold. NADP is surrounded by positively charged residues, and Gly-38 and Arg-39 are crucial for NADP binding. Site-directed mutagenesis studies suggest that Ser-150, Tyr-164, and Lys-168 located around the Rossmann fold constitute the catalytic triad. To our knowledge, this is the first report on molecular cloning and structure determination of a bacterial DEH reductase responsible for alginate metabolism.
-===Crystal structure of aldose reductase A1-R complexed with NADP===
+Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1.,Takase R, Ochiai A, Mikami B, Hashimoto W, Murata K Biochim Biophys Acta. 2010 May 27. PMID:20685299<ref>PMID:20685299</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3afn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20685299}}, adds the Publication Abstract to the page
+*[[Aldose reductase 3D structures|Aldose reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20685299 is the PubMed ID number.
+*[[Carbonyl reductase 3D structures|Carbonyl reductase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_20685299}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-AFN is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AFN OCA].
+[[Category: Large Structures]]
+[[Category: Sphingomonas sp. A1]]
-==Reference==
+[[Category: Hashimoto W]]
-<ref group="xtra">PMID:20685299</ref><references group="xtra"/>
+[[Category: Mikami B]]
-[[Category: 2-dehydro-3-deoxy-D-gluconate 6-dehydrogenase]]
+[[Category: Murata K]]
-[[Category: Sphingomonas sp.]]
+[[Category: Ochiai A]]
-[[Category: Hashimoto, W.]]
+[[Category: Takase R]]
-[[Category: Mikami, B.]]
-[[Category: Murata, K.]]
-[[Category: Ochiai, A.]]
-[[Category: Takase, R.]]
-[[Category: Alpha/beta/alpha]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann-fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:04:47 2010''