4PVQ

Crystal structure of sulfate-bound human l-asparaginase protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis.

Nomme, J.Su, Y.Konrad, M.Lavie, A.

(2012) Biochemistry 51: 6816-6826

  • DOI: 10.1021/bi300870g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Asparaginases catalyze the hydrolysis of the amino acid asparagine to aspartate and ammonia. Bacterial asparaginases are used in cancer chemotherapy to deplete asparagine from the blood, because several hematological malignancies depend on extracellu ...

    Asparaginases catalyze the hydrolysis of the amino acid asparagine to aspartate and ammonia. Bacterial asparaginases are used in cancer chemotherapy to deplete asparagine from the blood, because several hematological malignancies depend on extracellular asparagine for growth. To avoid the immune response against the bacterial enzymes, it would be beneficial to replace them with human asparaginases. However, unlike the bacterial asparaginases, the human enzymes have a millimolar K(m) value for asparagine, making them inefficient in depleting the amino acid from blood. To facilitate the development of human variants suitable for therapeutic use, we determined the structure of human l-asparaginase (hASNase3). This asparaginase is an N-terminal nucleophile (Ntn) family member that requires autocleavage between Gly167 and Thr168 to become catalytically competent. For most Ntn hydrolases, this autoproteolytic activation occurs efficiently. In contrast, hASNas3 is relatively stable in its uncleaved state, and this allowed us to observe the structure of the enzyme prior to cleavage. To determine the structure of the cleaved state, we exploited our discovery that the free amino acid glycine promotes complete cleavage of hASNase3. Both enzyme states were elucidated in the absence and presence of the product aspartate. Together, these structures provide insight into the conformational changes required for cleavage and the precise enzyme-substrate interactions. The new understanding of hASNase3 will serve to guide the design of variants that possess a decreased K(m) value for asparagine, making the human enzyme a suitable replacement for the bacterial asparaginases in cancer therapy.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isoaspartyl peptidase/L-asparaginase
A, B
310Homo sapiensMutation(s): 0 
Gene Names: ASRGL1 (ALP, CRASH)
EC: 3.4.19.5, 3.5.1.1
Find proteins for Q7L266 (Homo sapiens)
Go to Gene View: ASRGL1
Go to UniProtKB:  Q7L266
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.166 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 59.220α = 90.00
b = 59.220β = 90.00
c = 298.500γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata scaling
CrystalCleardata collection
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-18 
  • Released Date: 2014-03-26 
  • Deposition Author(s): Nomme, J., Lavie, A.
  • This entry supersedes: 4GDU

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release