7OS3

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV solved by S-SAD (orthorhombic form START)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site.

Loch, J.I.Imiolczyk, B.Sliwiak, J.Wantuch, A.Bejger, M.Gilski, M.Jaskolski, M.

(2021) Nat Commun 12: 6717-6717

  • DOI: https://doi.org/10.1038/s41467-021-27105-x
  • Primary Citation of Related Structures:  
    7OS3, 7OS5, 7OS6, 7OU1, 7OZ6

  • PubMed Abstract: 

    Rhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes an essential L-asparaginase (ReAV) with no sequence homology to known enzymes with this activity. High-resolution crystal structures of ReAV show indeed a structurally distinct, dimeric enzyme, with some resemblance to glutaminases and β-lactamases. However, ReAV has no glutaminase or lactamase activity, and at pH 9 its allosteric asparaginase activity is relatively high, with K m for L-Asn at 4.2 mM and k cat of 438 s -1 . The active site of ReAV, deduced from structural comparisons and confirmed by mutagenesis experiments, contains a highly specific Zn 2+ binding site without a catalytic role. The extensive active site includes residues with unusual chemical properties. There are two Ser-Lys tandems, all connected through a network of H-bonds to the Zn center, and three tightly bound water molecules near Ser48, which clearly indicate the catalytic nucleophile.


  • Organizational Affiliation

    Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase II proteinA [auth AAA],
B [auth BBB]
373Rhizobium etli CFN 42Mutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.15α = 90
b = 91.05β = 90
c = 105.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing

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: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection