5B5U image
Deposition Date 2016-05-23
Release Date 2017-05-31
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5B5U
Keywords:
Title:
Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.61 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:L-asparaginase
Gene (Uniprot):PF2047
Chain IDs:A
Chain Length:178
Number of Molecules:1
Biological Source:Pyrococcus furiosus DSM 3638
Polymer Type:polypeptide(L)
Molecule:L-asparaginase
Gene (Uniprot):PF2047
Chain IDs:B
Chain Length:127
Number of Molecules:1
Biological Source:Pyrococcus furiosus DSM 3638
Polymer Type:polypeptide(L)
Molecule:LEU-VAL-VAL-ASN
Chain IDs:C, D (auth: E)
Chain Length:4
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Primary Citation
Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property.
Sci Rep 10 21702 21702 (2020)
PMID: 33303914 DOI: 10.1038/s41598-020-78877-z

Abstact

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 β-strand in N-terminal domain, Leu179-Val-Val-Asn182 (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.

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Primary Citation of related structures