This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2q99

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:12, 25 June 2021) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2q99.png|left|200px]]
 
-
<!--
+
==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae==
-
The line below this paragraph, containing "STRUCTURE_2q99", creates the "Structure Box" on the page.
+
<StructureSection load='2q99' size='340' side='right'caption='[[2q99]], [[Resolution|resolution]] 1.64&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'>[[2q99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q99 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
-->
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LYS1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-
{{STRUCTURE_2q99| PDB=2q99 | SCENE= }}
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </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=2q99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q99 OCA], [https://pdbe.org/2q99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q99 RCSB], [https://www.ebi.ac.uk/pdbsum/2q99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q99 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
 +
== 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/q9/2q99_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=2q99 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two domains with similar dinucleotide binding folds with a deep cleft at the interface. The structure reveals homology to alanine dehydrogenase, despite low primary sequence similarity. A model of the ternary complex of SDH, NAD, and saccharopine identifies residues Lys77 and Glu122 as potentially important for substrate binding and/or catalysis, consistent with a proton shuttle mechanism. Furthermore, the model suggests that a conformational change is required for catalysis and that residues Lys99 and Asp281 may be instrumental in mediating this change. Analysis of the crystal structure in the context of other homologous enzymes from pathogenic fungi and human sources sheds light into the suitability of SDH as a target for antimicrobial drug development.
-
===Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae===
+
Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae.,Burk DL, Hwang J, Kwok E, Marrone L, Goodfellow V, Dmitrienko GI, Berghuis AM J Mol Biol. 2007 Oct 26;373(3):745-54. Epub 2007 Aug 24. PMID:17854830<ref>PMID:17854830</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_17854830}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2q99" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 17854830 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17854830}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Atcc 18824]]
-
2Q99 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q99 OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Berghuis, A M]]
-
==Reference==
+
[[Category: Burk, D L]]
-
Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae., Burk DL, Hwang J, Kwok E, Marrone L, Goodfellow V, Dmitrienko GI, Berghuis AM, J Mol Biol. 2007 Oct 26;373(3):745-54. Epub 2007 Aug 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17854830 17854830]
+
-
[[Category: Saccharomyces cerevisiae]]
+
-
[[Category: Single protein]]
+
-
[[Category: Berghuis, A M.]]
+
-
[[Category: Burk, D L.]]
+
[[Category: Alpha-aminoadipate pathway]]
[[Category: Alpha-aminoadipate pathway]]
[[Category: Alpha/beta protein]]
[[Category: Alpha/beta protein]]
Line 34: Line 44:
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold]]
[[Category: Rossmann fold]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:29:48 2008''
 

Current revision

Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae

PDB ID 2q99

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q99"
Personal tools