9QCU | pdb_00009qcu

Crystal structure of Rhizobium etli L-asparaginase ReAV S48A mutant

PDB DOI: https://doi.org/10.2210/pdb9QCU/pdb

Classification: HYDROLASE
Organism(s): Rhizobium etli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-03-05 Released: 2025-07-16
Deposition Author(s): Pokrywka, K., Grzechowiak, M., Loch, J.I., Ruszkowski, M., Gilski, M., Jaskolski, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.179 (Depositor), 0.178 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Probing the Active Site of Class 3 L-Asparaginase by Mutagenesis: Mutations of the Ser-Lys Tandems of ReAV.

Pokrywka, K., Grzechowiak, M., Sliwiak, J., Worsztynowicz, P., Loch, J.I., Ruszkowski, M., Gilski, M., Jaskolski, M.

(2025) Biomolecules 15

PubMed: 40723816 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/biom15070944
Primary Citation Related Structures:
9QCT, 9QCU, 9QCW, 9QCY, 9QCZ

PubMed Abstract:
The ReAV enzyme from Rhizobium etli , a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly specific zinc-binding site created by two cysteines, a lysine, and a water molecule. Two Ser-Lys tandems (Ser48-Lys51, Ser80-Lys263) are located in the close proximity of the metal binding site, with Ser48 hypothesized to be the catalytic nucleophile. To further investigate the catalytic process of ReAV, site-directed mutagenesis was employed to introduce alanine substitutions at residues from the Ser-Lys tandems and at Arg47, located near the Ser48-Lys51 tandem. These mutational studies, along with enzymatic assays and X-ray structure determinations, demonstrated that substitution of each of these highly conserved residues abolished the catalytic activity, confirming their essential role in enzyme mechanism.

Organizational Affiliation

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

Macromolecule Content

Total Structure Weight: 80.49 kDa
Atom Count: 6,412
Modeled Residue Count: 720
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase II	A, B	373	Rhizobium etli	Mutation(s): 1 Gene Names: ansA
UniProt
Find proteins for Q9RFN5 (Rhizobium etli) Explore Q9RFN5 Go to UniProtKB: Q9RFN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RFN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A]	E [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A]	C [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain K [auth A] mmCIF format, chain V [auth B] mmCIF format, chain K [auth A]	K [auth A], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] F [auth A] G [auth A] H [auth A] J [auth A] D [auth A], F [auth A], G [auth A], H [auth A], J [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A]	M [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain W [auth B]