9THY | pdb_00009thy

ReAIV structure containing an acrylamide adduct at Cys183 and an orthoborate ester at Ser47

PDB DOI: https://doi.org/10.2210/pdb9THY/pdb

Classification: HYDROLASE
Organism(s): Rhizobium etli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-04 Released: 2026-05-27
Deposition Author(s): Sliwiak, J., Grzechowiak, M., Worsztynowicz, P., Pokrywka, K., 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:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.137 (Depositor), 0.139 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Efficient acrylamide adduct formation suggests dual applications of ReAIV L-asparaginase.

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

(2026) Amino Acids

PubMed: 42113412 Search on PubMed
DOI: https://doi.org/10.1007/s00726-026-03525-1
Primary Citation Related Structures:
9THY

PubMed Abstract:
Isothermal titration calorimetry (ITC) studies of the enzyme kinetics and substrate specificity of Rhizobium etli Class 3 L-asparaginases, ReAIV (constitutive) and ReAV (inducible), showed that despite highly conserved catalytic site, the two isoforms differ significantly in thermostability, zinc affinity, and biochemical properties. As part of a wider investigation of potential non-natural substrates, acrylamide was tested, revealing a pronounced heat effect with ReAIV but none with ReAV. Crystallographic analysis showed the formation of a Michael adduct between acrylamide and a surface-exposed cysteine 183 in ReAIV, while the catalytic activity toward L-asparagine hydrolysis remained unaffected. These findings highlight the unique and multimodal reactivity of ReAIV, suggesting its potential dual application in the food industry: in selective removal of L-asparagine and in covalent sequestration of acrylamide under mild conditions. The acrylamide modification improved crystal morphology of ReAIV, offering practical advantages for structural studies. Additionally, a covalent modification of the catalytic Ser47 residue was observed in the presented crystal structure. Based on B-factor analysis, literature data, and detection of borate contamination in the laboratory water, this modification was interpreted as an orthoborate ester.

Organizational Affiliation

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. sliwiak@ibch.poznan.pl.

Macromolecule Content

Total Structure Weight: 73.37 kDa
Atom Count: 6,039
Modeled Residue Count: 678
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase II protein	A, B	341	Rhizobium etli	Mutation(s): 0 Gene Names: RHE_CH01144
UniProt
Find proteins for Q2KB35 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KB35 Go to UniProtKB: Q2KB35
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2KB35
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ROP (Subject of Investigation/LOI) Query on ROP Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Y [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Y [auth B]	P [auth A], Y [auth B]	PROPIONAMIDE C₃ H₇ N O QLNJFJADRCOGBJ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Y [auth B] Interactions & Density Focus chain P [auth A] Focus chain Y [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain V [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A]	K [auth A], L [auth A], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] 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 D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] 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 E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]