9QCY | pdb_00009qcy

Crystal structure of Rhizobium etli L-asparaginase ReAV S80A mutant

PDB DOI: https://doi.org/10.2210/pdb9QCY/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: 1.70 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.205 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/biom15070944
Primary Citation of 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: 161.04 kDa
Atom Count: 11,594
Modeled Residue Count: 1,394
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase II	A, B, C, D	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 F [auth A] SDF format, chain QA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain QA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain QA [auth D]	F [auth A], QA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain QA [auth D] Interactions & Density Focus chain F [auth A] Focus chain QA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain Z [auth C]	E [auth A], KA [auth D], L [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain KA [auth D] Focus chain L [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain KA [auth D] Focus chain L [auth B] Focus chain Z [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain RA [auth D] SDF format, chain Y [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain Y [auth B]	IA [auth C], K [auth A], RA [auth D], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain K [auth A] Focus chain RA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth C] Focus chain K [auth A] Focus chain RA [auth D] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], LA [auth D], M [auth B], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], R [auth B], S [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain JA [auth C]	JA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]