Structure of atypical asparaginase from Rhodospirillum rubrum (mutant K19E)

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report

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RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.

Zhang, D.Czapinska, H.Bochtler, M.Wlodawer, A.Lubkowski, J.

(2024) Protein Sci 33: e4920-e4920

  • DOI: https://doi.org/10.1002/pro.4920
  • Primary Citation of Related Structures:  
    8UOO, 8UOR, 8UOU, 8UOW, 8UP3, 8UP6, 8UP7, 8UP8, 8UP9, 8UPC

  • PubMed Abstract: 

    L-Asparaginases (ASNases) catalyze the hydrolysis of L-Asn to L-Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300-400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum, reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N-terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L-Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short-chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild-type RrA, both with and without bound L-Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand-alone subfamily of ASNases that can catalyze the hydrolysis of L-Asn to L-Asp despite the lack of the C-terminal domain that is present in all ASNases described structurally to date.

  • Organizational Affiliation

    Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
185Rhodospirillum rubrum ATCC 11170Mutation(s): 1 
Gene Names: Rru_A3730
Find proteins for Q2RMX1 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RMX1 
Go to UniProtKB:  Q2RMX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RMX1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.581α = 90
b = 77.435β = 90
c = 57.758γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release