2ez9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:41, 23 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2ez9.png|left|200px]]
 
-
<!--
+
==Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate==
-
The line below this paragraph, containing "STRUCTURE_2ez9", creates the "Structure Box" on the page.
+
<StructureSection load='2ez9' size='340' side='right'caption='[[2ez9]], [[Resolution|resolution]] 1.60&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'>[[2ez9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZ9 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]] 1.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TDK:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>TDK</scene></td></tr>
-
{{STRUCTURE_2ez9| PDB=2ez9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ez9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ez9 OCA], [https://pdbe.org/2ez9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ez9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ez9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ez9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/POXB_LACPL POXB_LACPL] Important for the aerobic growth. Decarboxylates pyruvate in four steps. The energy released is partially stored in acetyl phosphate.
 +
== 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/ez/2ez9_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=2ez9 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Enzymes that use the cofactor thiamin diphosphate (ThDP, 1), the biologically active form of vitamin B(1), are involved in numerous metabolic pathways in all organisms. Although a theory of the cofactor's underlying reaction mechanism has been established over the last five decades, the three-dimensional structures of most major reaction intermediates of ThDP enzymes have remained elusive. Here, we report the X-ray structures of key intermediates in the oxidative decarboxylation of pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP- and flavin-dependent enzyme pyruvate oxidase (POX)3 from Lactobacillus plantarum. The structures of 2-lactyl-ThDP (LThDP, 2) and its stable phosphonate analog, of 2-hydroxyethyl-ThDP (HEThDP, 3) enamine and of 2-acetyl-ThDP (AcThDP, 4; all shown bound to the enzyme's active site) provide profound insights into the chemical mechanisms and the stereochemical course of thiamin catalysis. These snapshots also suggest a mechanism for a phosphate-linked acyl transfer coupled to electron transfer in a radical reaction of pyruvate oxidase.
-
===Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate===
+
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.,Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:16680160<ref>PMID:16680160</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_16680160}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2ez9" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 16680160 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16680160}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Lactiplantibacillus plantarum]]
-
2EZ9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZ9 OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Golbik R]]
-
==Reference==
+
[[Category: Hinze E]]
-
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography., Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K, Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16680160 16680160]
+
[[Category: Meyer D]]
-
[[Category: Lactobacillus plantarum]]
+
[[Category: Steinmetz A]]
-
[[Category: Pyruvate oxidase]]
+
[[Category: Tittmann K]]
-
[[Category: Single protein]]
+
[[Category: Wille G]]
-
[[Category: Golbik, R.]]
+
-
[[Category: Hinze, E.]]
+
-
[[Category: Meyer, D.]]
+
-
[[Category: Steinmetz, A.]]
+
-
[[Category: Tittmann, K.]]
+
-
[[Category: Wille, G.]]
+
-
[[Category: Reaction intermediate analogue]]
+
-
[[Category: Tpp enzyme]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:34:25 2008''
+

Current revision

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate

PDB ID 2ez9

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/2ez9"
Personal tools