8RUE

Crystal structure of Rhizobium etli L-asparaginase ReAV H139A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

Starting Model: experimental
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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. I. Tinkering with the zinc coordination site of ReAV.

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

(2024) Front Chem 12: 1381032-1381032

  • DOI: https://doi.org/10.3389/fchem.2024.1381032
  • Primary Citation of Related Structures:  
    8RUA, 8RUD, 8RUE, 8RUF, 8RUG

  • PubMed Abstract: 

    ReAV, the inducible Class-3 L-asparaginase from the nitrogen-fixing symbiotic bacterium Rhizobium etli , is an interesting candidate for optimizing its enzymatic potential for antileukemic applications. Since it has no structural similarity to known enzymes with this activity, it may offer completely new ways of approach. Also, as an unrelated protein, it would evade the immunological response elicited by other asparaginases. The crystal structure of ReAV revealed a uniquely assembled protein homodimer with a highly specific C135/K138/C189 zinc binding site in each subunit. It was also shown before that the Zn 2+ cation at low and optimal concentration boosts the ReAV activity and improves substrate specificity, which indicates its role in substrate recognition. However, the detailed catalytic mechanism of ReAV is still unknown. In this work, we have applied site-directed mutagenesis coupled with enzymatic assays and X-ray structural analysis to elucidate the role of the residues in the zinc coordination sphere in catalysis. Almost all of the seven ReAV muteins created in this campaign lost the ability to hydrolyze L-asparagine, confirming our predictions about the significance of the selected residues in substrate hydrolysis. We were able to crystallize five of the ReAV mutants and solve their crystal structures, revealing some intriguing changes in the active site area as a result of the mutations. With alanine substitutions of Cys135 or Cys189, the zinc coordination site fell apart and the mutants were unable to bind the Zn 2+ cation. Moreover, the absence of Lys138 induced atomic shifts and conformational changes of the neighboring residues from two active-site Ser-Lys tandems. Ser48 from one of the tandems, which is hypothesized to be the catalytic nucleophile, usually changes its hydration pattern in response to the mutations. Taken together, the results provide many useful clues about the catalytic mechanism of the enzyme, allowing one to cautiously postulate a possible enzymatic scenario.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase II protein
A, B, C, D
373Rhizobium etliMutation(s): 1 
Gene Names: ansARHE_PE00350
UniProt
Find proteins for Q2K0Z2 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42))
Explore Q2K0Z2 
Go to UniProtKB:  Q2K0Z2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2K0Z2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
HA [auth D],
U [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
JA [auth D],
P [auth B],
R [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
GA [auth D],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth D],
M [auth A],
O [auth B],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
EA [auth D]
F [auth A]
FA [auth D]
AA [auth C],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
H [auth A],
I [auth A],
IA [auth D],
LA [auth D],
MA [auth D],
Q [auth B],
S [auth B],
T [auth B],
W [auth B],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
J [auth A]
K [auth A]
KA [auth D]
BA [auth C],
CA [auth C],
J [auth A],
K [auth A],
KA [auth D],
L [auth A],
X [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.906α = 90
b = 91.472β = 96.98
c = 114.471γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2020/37/B/NZ1/03250

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references