9QCZ | pdb_00009qcz

Crystal structure of Rhizobium etli L-asparaginase ReAV K263A mutant

PDB DOI: https://doi.org/10.2210/pdb9QCZ/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: 1.60 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.161 (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: 161.95 kDa
Atom Count: 12,447
Modeled Residue Count: 1,399
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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(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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C] mmCIF format, chain OA [auth C]	OA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain OA [auth C] Interactions & Density Focus chain OA [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain XA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain XA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain XA [auth D]	GA [auth C], N [auth A], T [auth B], XA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain GA [auth C] Focus chain N [auth A] Focus chain T [auth B] Focus chain XA [auth D] Interactions & Density Focus chain GA [auth C] Focus chain N [auth A] Focus chain T [auth B] Focus chain XA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain NA [auth C] SDF format, chain UA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain UA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain UA [auth D]	K [auth A], NA [auth C], UA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain NA [auth C] Focus chain UA [auth D] Interactions & Density Focus chain K [auth A] Focus chain NA [auth C] Focus chain UA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain TA [auth D] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain MA [auth C] SDF format, chain H [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain H [auth A]	DA [auth C] EA [auth C] H [auth A] L [auth A] LA [auth C] DA [auth C], EA [auth C], H [auth A], L [auth A], LA [auth C], MA [auth C], RA [auth D], S [auth B], TA [auth D], V [auth B], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain H [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain RA [auth D] Focus chain S [auth B] Focus chain TA [auth D] Focus chain V [auth B] Focus chain Y [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain H [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain RA [auth D] Focus chain S [auth B] Focus chain TA [auth D] Focus chain V [auth B] Focus chain Y [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain PA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	O [auth A], PA [auth C], Z [auth B], ZA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain PA [auth C] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain O [auth A] Focus chain PA [auth C] Focus chain Z [auth B] Focus chain ZA [auth D]
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 FA [auth C] SDF format, chain G [auth A] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain SA [auth D] SDF format, chain U [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain YA [auth D] SDF format, chain WA [auth D] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	AA [auth C] BA [auth C] CA [auth C] E [auth A] F [auth A] AA [auth C], BA [auth C], CA [auth C], E [auth A], F [auth A], FA [auth C], G [auth A], HA [auth C], IA [auth C], JA [auth C], KA [auth C], M [auth A], Q [auth B], QA [auth D], R [auth B], SA [auth D], U [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], YA [auth D]	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 E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain SA [auth D] Focus chain U [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain YA [auth D] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain SA [auth D] Focus chain U [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain YA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain P [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain P [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain P [auth A]	AB [auth D], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth D] Focus chain P [auth A] Interactions & Density Focus chain AB [auth D] Focus chain P [auth A]