4OSX | pdb_00004osx

STRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb4OSX/pdb
• Entry: 4OSX supersedes: 4HLO

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-13 Released: 2014-03-05 
• Deposition Author(s): Nomme, J., Lavie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Free Glycine Accelerates the Autoproteolytic Activation of Human Asparaginase.

Su, Y., Karamitros, C.S., Nomme, J., Mcsorley, T., Konrad, M., Lavie, A.

(2013) Chem Biol 20: 533

• PubMed: 23601642 
• DOI: https://doi.org/10.1016/j.chembiol.2013.03.006
• Primary Citation Related Structures: 
  4OSX, 4OSY


• PubMed Abstract: 
  

  Human asparaginase 3 (hASNase3), which belongs to the N-terminal nucleophile hydrolase superfamily, is synthesized as a single polypeptide that is devoid of asparaginase activity. Intramolecular autoproteolytic processing releases the amino group of Thr168, a moiety required for catalyzing asparagine hydrolysis. Recombinant hASNase3 purifies as the uncleaved, asparaginase-inactive form and undergoes self-cleavage to the active form at a very slow rate. Here, we show that the free amino acid glycine selectively acts to accelerate hASNase3 cleavage both in vitro and in human cells. Other small amino acids such as alanine, serine, or the substrate asparagine are not capable of promoting autoproteolysis. Crystal structures of hASNase3 in complex with glycine in the uncleaved and cleaved enzyme states reveal the mechanism of glycine-accelerated posttranslational processing and explain why no other amino acid can substitute for glycine.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.89 kDa 
• Atom Count: 4,598 
• Modeled Residue Count: 600 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoaspartyl peptidase/L-asparaginase	A, B	309	Homo sapiens	Mutation(s): 0  Gene Names: ALP, ASRGL1, CRASH EC: 3.4.19.5 (PDB Primary Data), 3.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L266 (Homo sapiens) Explore Q7L266  Go to UniProtKB:  Q7L266
PHAROS:  Q7L266 GTEx:  ENSG00000162174

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLY	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
NA	C [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.94	α = 90
b = 59.94	β = 90
c = 301.1	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Nomme, J., Lavie, A.
• This entry supersedes: 4HLO

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description