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.


5b5u

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "5b5u" [edit=sysop:move=sysop])
Current revision (16:01, 8 November 2023) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 5b5u is ON HOLD
+
==Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide==
 +
<StructureSection load='5b5u' size='340' side='right'caption='[[5b5u]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[5b5u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] and [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B5U FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></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=5b5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b5u OCA], [https://pdbe.org/5b5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b5u RCSB], [https://www.ebi.ac.uk/pdbsum/5b5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b5u ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ASPG_PYRFU ASPG_PYRFU] Catalyzes the hydrolysis of L-asparagine into L-aspartate and ammonia. Displays no glutaminase activity, a highly desirable therapeutic property.<ref>PMID:20370616</ref> <ref>PMID:22166247</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
It remains undeciphered how thermophilic enzymes display enhanced stability at elevated temperatures. Taking L-asparaginase from P. furiosus (PfA) as an example, we combined scattering shapes deduced from small-angle X-ray scattering (SAXS) data at increased temperatures with symmetry mates from crystallographic structures to find that heating caused end-to-end association. The small contact point of self-binding appeared to be enabled by a terminal short beta-strand in N-terminal domain, Leu(179)-Val-Val-Asn(182) (LVVN). Interestingly, deletion of this strand led to a defunct enzyme, whereas suplementation of the peptide LVVN to the defunct enzyme restored structural frameworkwith mesophile-type functionality. Crystal structure of the peptide-bound defunct enzyme showed that one peptide ispresent in the same coordinates as in original enzyme, explaining gain-of lost function. A second peptide was seen bound to the protein at a different location suggesting its possible role in substrate-free molecular-association. Overall, we show that the heating induced self-assembly of native shapes of PfA led to an apparent super-stable assembly.
-
Authors:
+
Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property.,Sharma P, Tomar R, Yadav SS, Badmalia MD, Nath SK, Ashish, Kundu B Sci Rep. 2020 Dec 10;10(1):21702. doi: 10.1038/s41598-020-78877-z. PMID:33303914<ref>PMID:33303914</ref>
-
Description:
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[Category: Unreleased Structures]]
+
</div>
 +
<div class="pdbe-citations 5b5u" style="background-color:#fffaf0;"></div>
 +
 
 +
==See Also==
 +
*[[Asparaginase 3D structures|Asparaginase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Pyrococcus furiosus]]
 +
[[Category: Pyrococcus furiosus DSM 3638]]
 +
[[Category: Ashish F]]
 +
[[Category: Kundu B]]
 +
[[Category: Nath SK]]
 +
[[Category: Sharma P]]
 +
[[Category: Tomar R]]

Current revision

Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide

PDB ID 5b5u

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools