8ECD | pdb_00008ecd

E. coli L-asparaginase II mutant (V27T) in complex with L-Asp

PDB DOI: https://doi.org/10.2210/pdb8ECD/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-09-01 Released: 2022-11-16
Deposition Author(s): Strzelczyk, P., Wlodawer, A., Lubkowski, J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.164 (Depositor), 0.170 (DCC)
R-Value Work:
0.127 (Depositor), 0.133 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The E. coli L-asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions.

Strzelczyk, P., Zhang, D., Wlodawer, A., Lubkowski, J.

(2022) FEBS Lett 596: 3060-3068

PubMed: 36310372 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.14526
Primary Citation Related Structures:
8ECD, 8ECE

PubMed Abstract:
Bacterial L-asparaginases have been used for over 40 years as anticancer drugs. Ardalan et al. (Medical Hypotheses 112, 7-17, 2018) proposed that the V27T mutant of Escherichia coli type II L-asparaginase, EcAII(V27T), should display altered biophysical and catalytic properties compared to the wild-type enzyme, EcAII(wt), rendering it more favourable as a pharmaceutical. They postulated that EcAII(V27T) would exhibit reduced glutaminolytic activity and be more stable compared to EcAII(wt). Their postulates, however, were purely theoretical. Here, we characterized experimentally selected properties of EcAII(V27T). We found asparaginolytic activity of this mutant unchanged, whereas its glutaminolytic activity was fourfold lower compared with EcAII(wt). We did not observe significant differences in stabilities of EcAII(wt) and EcAII(V27T). Crystal structures of the complexes with L-Asp and L-Glu showed considerable differences in binding modes of both substrates.

Organizational Affiliation

Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.

Macromolecule Content

Total Structure Weight: 145.12 kDa
Atom Count: 11,603
Modeled Residue Count: 1,309
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase 2	A, B, C, D	334	Escherichia coli K-12	Mutation(s): 1 Gene Names: ansB, b2957, JW2924 EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805 Go to UniProtKB: P00805
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00805
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain V [auth D]	U [auth C], V [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Focus chain V [auth D] Interactions & Density Focus chain U [auth C] Focus chain V [auth D]
ASP (Subject of Investigation/LOI) Query on ASP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain W [auth D]	E [auth A], I [auth B], M [auth C], W [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain X [auth D]	AA [auth D] CA [auth D] F [auth A] J [auth B] K [auth B] AA [auth D], CA [auth D], F [auth A], J [auth B], K [auth B], N [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	BA [auth D] G [auth A] H [auth A] L [auth B] O [auth C] BA [auth D], G [auth A], H [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]