5B5U | pdb_00005b5u

Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide

PDB DOI: https://doi.org/10.2210/pdb5B5U/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus furiosus DSM 3638, Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-05-23 Released: 2017-05-31
Deposition Author(s): Sharma, P., Tomar, R., Nath, S.K., Kundu, B., Ashish, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.242 (Depositor), 0.234 (DCC)
R-Value Work:
0.203 (Depositor), 0.202 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property.

Sharma, P., Tomar, R., Yadav, S.S., Badmalia, M.D., Nath, S.K., Kundu, B.

(2020) Sci Rep 10: 21702-21702

PubMed: 33303914 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-020-78877-z
Primary Citation Related Structures:
5B5U, 5B74, 5CBP

PubMed Abstract:
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, 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.

Organizational Affiliation

CSIR-Institute of Microbial Technology, Sec 39 A, Chandigarh, 160036, India.

Macromolecule Content

Total Structure Weight: 34.86 kDa
Atom Count: 2,436
Modeled Residue Count: 310
Deposited Residue Count: 313
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	A	178	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF2047 EC: 3.5.1.1
UniProt
Find proteins for Q8TZE8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZE8 Go to UniProtKB: Q8TZE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZE8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	B	127	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF2047 EC: 3.5.1.1
UniProt
Find proteins for Q8TZE8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZE8 Go to UniProtKB: Q8TZE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZE8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LEU-VAL-VAL-ASN	C, D [auth E]	4	Pyrococcus furiosus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]