3wdm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:44, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis==
==Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis==
-
<StructureSection load='3wdm' size='340' side='right' caption='[[3wdm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='3wdm' size='340' side='right'caption='[[3wdm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3wdm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WDM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3wdm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WDM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene></td></tr>
+
</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&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wdk|3wdk]], [[3wdl|3wdl]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-phosphopantoate--beta-alanine_ligase 4-phosphopantoate--beta-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.36 6.3.2.36] </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=3wdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdm OCA], [https://pdbe.org/3wdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wdm RCSB], [https://www.ebi.ac.uk/pdbsum/3wdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdm ProSAT]</span></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdm OCA], [http://pdbe.org/3wdm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wdm RCSB], [http://www.ebi.ac.uk/pdbsum/3wdm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdm ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/PPS_THEKO PPS_THEKO]] Catalyzes the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. Cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase (PS) activity.
+
[https://www.uniprot.org/uniprot/PPS_THEKO PPS_THEKO] Catalyzes the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. Cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase (PS) activity.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Bacteria/eukaryotes share a common pathway for coenzyme A biosynthesis which involves two enzymes to convert pantoate to 4'-phosphopantothenate. These two enzymes are absent in almost all archaea. Recently, it was reported that two novel enzymes, pantoate kinase (PoK) and phosphopantothenate synthetase (PPS), are responsible for this conversion in archaea. Here, we report the crystal structure of PPS from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complexes with substrates, ATP, and ATP and 4-phosphopantoate (PPo). PPS forms an asymmetric homodimer, in which two monomers composing a dimer, deviated from the exact 2-fold symmetry, displaying 4 degrees -13 degrees distortion. The structural features are consistent with the mutagenesis data and the results of biochemical experiments previously reported. Based on these structures, we discuss the catalytic mechanism by which PPS produces phosphopantoyl adenylate (PPA), which is thought to be a reaction intermediate. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.
+
-
 
+
-
Crystal Structure of Phosphopantothenate Synthetase from Thermococcus k odakarensis.,Kishimoto A, Kita A, Ishibashi T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K Proteins. 2014 Mar 17. doi: 10.1002/prot.24546. PMID:24638914<ref>PMID:24638914</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3wdm" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 4-phosphopantoate--beta-alanine ligase]]
+
[[Category: Large Structures]]
-
[[Category: Atomi, H]]
+
[[Category: Thermococcus kodakarensis KOD1]]
-
[[Category: Imanaka, T]]
+
[[Category: Atomi H]]
-
[[Category: Ishibashi, T]]
+
[[Category: Imanaka T]]
-
[[Category: Kishimoto, A]]
+
[[Category: Ishibashi T]]
-
[[Category: Kita, A]]
+
[[Category: Kishimoto A]]
-
[[Category: Miki, K]]
+
[[Category: Kita A]]
-
[[Category: Tomita, H]]
+
[[Category: Miki K]]
-
[[Category: Yokooji, Y]]
+
[[Category: Tomita H]]
-
[[Category: Ligase]]
+
[[Category: Yokooji Y]]

Current revision

Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis

PDB ID 3wdm

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/3wdm"
Personal tools