2q2v: Difference between revisions

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-{{Seed}}
-[[Image:2q2v.png|left|200px]]
-<!--
+==Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida==
-The line below this paragraph, containing "STRUCTURE_2q2v", creates the "Structure Box" on the page.
+<StructureSection load='2q2v' size='340' side='right'caption='[[2q2v]], [[Resolution|resolution]] 1.90&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'>[[2q2v]] is a 4 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=2Q2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2V 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]] 1.9&#8491;</td></tr>
--->
+<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></td></tr>
-{{STRUCTURE_2q2v|  PDB=2q2v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2v OCA], [https://pdbe.org/2q2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2v RCSB], [https://www.ebi.ac.uk/pdbsum/2q2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9AE70_PSEPU Q9AE70_PSEPU]
+== 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/q2/2q2v_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=2q2v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+D-3-Hydroxybutyrate dehydrogenase from Pseudomonas putida belongs to the family of short-chain dehydrogenases/reductases. We have determined X-ray structures of the D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida, which was recombinantly expressed in Escherichia coli, in three different crystal forms to resolutions between 1.9 and 2.1 A. The so-called substrate-binding loop (residues 187-210) was partially disordered in several subunits, in both the presence and absence of NAD(+). However, in two subunits, this loop was completely defined in an open conformation in the apoenzyme and in a closed conformation in the complex structure with NAD(+). Structural comparisons indicated that the loop moves as a rigid body by about 46 degrees . However, the two small alpha-helices (alphaFG1 and alphaFG2) of the loop also re-orientated slightly during the conformational change. Probably, the interactions of Val185, Thr187 and Leu189 with the cosubstrate induced the conformational change. A model of the binding mode of the substrate D-3-hydroxybutyrate indicated that the loop in the closed conformation, as a result of NAD(+) binding, is positioned competent for catalysis. Gln193 is the only residue of the substrate-binding loop that interacts directly with the substrate. A translation, libration and screw (TLS) analysis of the rigid body movement of the loop in the crystal showed significant librational displacements, describing the coordinated movement of the substrate-binding loop in the crystal. NAD(+) binding increased the flexibility of the substrate-binding loop and shifted the equilibrium between the open and closed forms towards the closed form. The finding that all NAD(+) -bound subunits are present in the closed form and all NAD(+) -free subunits in the open form indicates that the loop closure is induced by cosubstrate binding alone. This mechanism may contribute to the sequential binding of cosubstrate followed by substrate.
-===Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida===
+Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida.,Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N FEBS J. 2007 Nov;274(21):5767-79. PMID:17958702<ref>PMID:17958702</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q2v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17958702}}, adds the Publication Abstract to the page
+*[[Inositol polyphosphate 5-phosphatase OCRL|Inositol polyphosphate 5-phosphatase OCRL]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17958702 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17958702}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Q2V 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=2Q2V OCA].
-==Reference==
-Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida., Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N, FEBS J. 2007 Nov;274(21):5767-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17958702 17958702]
-[[Category: 3-hydroxybutyrate dehydrogenase]]
-[[Category: Pseudomonas putida]]
-[[Category: Single protein]]
-[[Category: Feller, C.]]
-[[Category: Grunow, M.]]
-[[Category: Keim, A.]]
-[[Category: Kuettner, E B.]]
-[[Category: Paithankar, K S.]]
-[[Category: Strater, N.]]
-[[Category: D-3-hydroxybutyrate dehydrogenase]]
-[[Category: Oxidoreductase]]
 [[Category: Pseudomonas putida]]
-[[Category: Sdr]]
+[[Category: Feller C]]
+[[Category: Grunow M]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:10:06 2008''
+[[Category: Keim A]]
+[[Category: Kuettner EB]]
+[[Category: Paithankar KS]]
+[[Category: Strater N]]