3asv: Difference between revisions

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[[Image:3asv.png|left|200px]]


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==The Closed form of serine dehydrogenase complexed with NADP+==
The line below this paragraph, containing "STRUCTURE_3asv", creates the "Structure Box" on the page.
<StructureSection load='3asv' size='340' side='right'caption='[[3asv]], [[Resolution|resolution]] 2.70&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'>[[3asv]] is a 6 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=3ASV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ASV 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]] 2.7&#8491;</td></tr>
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<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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_3asv|  PDB=3asv  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3asv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3asv OCA], [https://pdbe.org/3asv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3asv RCSB], [https://www.ebi.ac.uk/pdbsum/3asv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3asv ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Serine dehydrogenase from Escherichia coli is a homotetrameric enzyme belonging to the short-chain dehydrogenase/reductase (SDR) family. This enzyme catalyses the NADP(+)-dependent oxidation of serine to 2-aminomalonate semialdehyde. The enzyme shows a stereospecificity for beta-(3S)-hydroxy acid as a substrate; however, no stereospecificity was observed at the alpha-carbon. The structures of the ligand-free SerDH and SerDH-NADP(+)-phosphate complex were determined at 1.9 and 2.7 A resolutions, respectively. The overall structure, including the catalytic tetrad of Asn106, Ser134, Tyr147 and Lys151, shows obvious relationships with other members of the SDR family. The structure of the substrate-binding loop and that of the C-terminal region were disordered in the ligand-free enzyme, whereas these structures were clearly defined in the SerDH-NADP(+) complex as a closed form. Interestingly, the C-terminal region was protruded from the main body and it formed an anti-parallel beta-sheet with another C-terminal region on the subunit that is diagonally opposite to that in the tetramer. It is revealed that the C-terminal region possesses the important roles in substrate binding through the stabilization of the substrate-binding loop in the closed form complex. The roles of the C-terminal region along with those of the residues involved in substrate recognition were studied by site-directed mutagenesis.


===The Closed form of serine dehydrogenase complexed with NADP+===
Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation.,Yamazawa R, Nakajima Y, Mushiake K, Yoshimoto T, Ito K J Biochem. 2011 Jun;149(6):701-12. Epub 2011 Feb 23. PMID:21349860<ref>PMID:21349860</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_21349860}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3asv" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 21349860 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_21349860}}
__TOC__
 
</StructureSection>
==About this Structure==
[[3asv]] is a 6 chain structure with 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=3ASV OCA].
 
==Reference==
<ref group="xtra">PMID:021349860</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Ito, K.]]
[[Category: Large Structures]]
[[Category: Nakajima, Y.]]
[[Category: Ito K]]
[[Category: Yamazawa, R.]]
[[Category: Nakajima Y]]
[[Category: Yoshimoto, T.]]
[[Category: Yamazawa R]]
[[Category: L-allo-threonine dehydrogenase]]
[[Category: Yoshimoto T]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold]]
[[Category: Sdr family]]
[[Category: Short-chain dehydrogenase/reductase]]

Latest revision as of 15:54, 4 October 2023

The Closed form of serine dehydrogenase complexed with NADP+

3asv, resolution 2.70Å

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