6pcd: Difference between revisions

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<StructureSection load='6pcd' size='340' side='right'caption='[[6pcd]], [[Resolution|resolution]] 1.37&Aring;' scene=''>
<StructureSection load='6pcd' size='340' side='right'caption='[[6pcd]], [[Resolution|resolution]] 1.37&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6pcd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Psepk Psepk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PCD FirstGlance]. <br>
<table><tr><td colspan='2'>[[6pcd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PCD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=OYA:OCTANAL'>OYA</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]] 1.37&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pcaF-I, PP_1377 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160488 PSEPK])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=OYA:OCTANAL'>OYA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcd OCA], [http://pdbe.org/6pcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pcd RCSB], [http://www.ebi.ac.uk/pdbsum/6pcd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcd ProSAT]</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=6pcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcd OCA], [https://pdbe.org/6pcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pcd RCSB], [https://www.ebi.ac.uk/pdbsum/6pcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcd ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q88N39_PSEPK Q88N39_PSEPK]
Thiolases are a well characterized family of enzymes with two distinct categories: degradative, beta-ketoadipyl-CoA thiolases and biosynthetic, acetoacetyl-CoA thiolases. Both classes share an identical catalytic triad but catalyze reactions in opposite directions. Moreover, it is established that in contrast to the biosynthetic thiolases the degradative thiolases can accept substrates with broad chain lengths. Hitherto, no residue or structural pattern has been recognized that might help to discern the two thiolases, here we exploit, a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF, as a model system to understand features which distinguishes the two classes using structural studies and bioinformatics analyses. Degradative thiolases have different active site architecture when compared to biosynthetic thiolases, demonstrating the dissimilar chemical nature of the active site architecture. Both thiolases deploy different "anchoring residues" to tether the large Coenzyme A (CoA) or CoA derivatives. Interestingly, the H356 of the catalytic triad in PcaF is directly involved in tethering the CoA/CoA derivatives into the active site and we were able to trap a gridlocked thiolase structure of the H356A mutant, where the CoA was found to be covalently linked to the catalytic cysteine residue, inhibiting the overall reaction. Further, X-ray structures with two long chain CoA derivatives, hexanal-CoA and octanal-CoA helped in delineating the long tunnel of 235 A(2) surface area in PcaF and led to identification of a unique covering loop exclusive to degradative thiolases that plays an active role in determining the tunnel length and the nature of the binding substrate.


Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase.,Bhaskar S, Steer DL, Anand R, Panjikar S J Struct Biol X. 2020 Jan 3;4:100018. doi: 10.1016/j.yjsbx.2019.100018., eCollection 2020. PMID:32647822<ref>PMID:32647822</ref>
==See Also==
 
*[[Thiolase 3D structures|Thiolase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6pcd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Psepk]]
[[Category: Pseudomonas putida KT2440]]
[[Category: Panjikar, S]]
[[Category: Panjikar S]]
[[Category: Sukritee, B]]
[[Category: Sukritee B]]
[[Category: Aromatic pollutant catabolism]]
[[Category: Degradative enzyme]]
[[Category: Transferase]]

Latest revision as of 17:54, 13 March 2024

Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex Octanoyl coenzyme ACrystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex Octanoyl coenzyme A

Structural highlights

6pcd is a 4 chain structure with sequence from Pseudomonas putida KT2440. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.37Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q88N39_PSEPK

See Also

6pcd, resolution 1.37Å

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