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3wdk

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Revision as of 09:33, 21 February 2019

Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate

Structural highlights

3wdk is a 4 chain structure with sequence from Pyrococcus kodakaraensis (strain kod1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3wdl, 3wdm
Gene:	TK1686 (Pyrococcus kodakaraensis (strain KOD1))
Activity:	4-phosphopantoate--beta-alanine ligase, with EC number 6.3.2.36
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kishimoto A, Kita A, Ishibashi T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K. Crystal Structure of Phosphopantothenate Synthetase from Thermococcus k odakarensis. Proteins. 2014 Mar 17. doi: 10.1002/prot.24546. PMID:24638914 doi:http://dx.doi.org/10.1002/prot.24546

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3wdk"

@@ Line 3: / Line 3: @@
 <StructureSection load='3wdk' size='340' side='right' caption='[[3wdk]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wdk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WDK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wdk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WDK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=PTJ:5-O-[(S)-HYDROXY{[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]OXY}PHOSPHORYL]ADENOSINE'>PTJ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wdl|3wdl]], [[3wdm|3wdm]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1686 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdk OCA], [http://pdbe.org/3wdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wdk RCSB], [http://www.ebi.ac.uk/pdbsum/3wdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdk ProSAT]</span></td></tr>

3wdk

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Revision as of 09:33, 21 February 2019

Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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