4ZM9

Crystal structure of circularly permuted human asparaginase-like protein 1

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2015-05-02 Released: 2016-02-17 
  • Deposition Author(s): Li, W.Z., Zhang, Y.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute; Cancer Prevention and Research Institute of Texas 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages.

Li, W.Irani, S.Crutchfield, A.Hodge, K.Matthews, W.Patel, P.Zhang, Y.J.Stone, E.

(2016) Biochemistry 55: 960-969

  • DOI: 10.1021/acs.biochem.5b01157

  • PubMed Abstract: 
  • The human asparaginase-like protein 1 (hASRGL1) is a member of the N-terminal nucleophile (Ntn) family that hydrolyzes l-asparagine and isoaspartyl-dipeptides. The nascent protein folds into an αβ-βα sandwich fold homodimer that cleaves its own pepti ...

    The human asparaginase-like protein 1 (hASRGL1) is a member of the N-terminal nucleophile (Ntn) family that hydrolyzes l-asparagine and isoaspartyl-dipeptides. The nascent protein folds into an αβ-βα sandwich fold homodimer that cleaves its own peptide backbone at the G167-T168 bond, resulting in the active form of the enzyme. However, biophysical studies of hASRGL1 are difficult because of the curious fact that intramolecular cleavage of the G167-T168 peptide bond reaches only ≤50% completion. We capitalized upon our previous observation that intramolecular processing increases thermostability and developed a differential scanning fluorimetry assay that allowed direct detection of distinct processing intermediates for the first time. A kinetic analysis of these intermediates revealed that cleavage of one subunit of the hASRGL1 subunit drastically reduces the processing rate of the adjacent monomer, and a mutagenesis study showed that stabilization of the dimer interface plays a critical role in this process. We also report a comprehensive analysis of conserved active site residues and delineate their relative roles in autoprocessing and substrate hydrolysis. In addition to glycine, which was previously reported to selectively accelerate hASRGL1 cleavage, we identified several novel small molecule activators that also promote intramolecular processing. The structure-activity analysis supports the hypothesis that multiple negatively charged small molecules interact within the active site of hASRGL1 to act as a base in promoting cleavage. Overall, our investigation provides a mechanistic understanding of the maturation process of this Ntn hydrolase family member.


    Organizational Affiliation

    Department of Molecular Biosciences, ‡Department of Chemical Engineering, and §Institute of Cellular and Molecular Biology, University of Texas , Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isoaspartyl peptidase/L-asparaginase
A, B, C, D
327Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, B, C, D
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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

Download SDF File 
Download CCD File 
A, B, C, D
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A, C
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
B, D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.308α = 90.00
b = 111.107β = 90.00
c = 122.517γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-05-02 
  • Released Date: 2016-02-17 
  • Deposition Author(s): Li, W.Z., Zhang, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01 CA154754
National Institutes of Health/National Cancer InstituteUnited StatesCA139059
Cancer Prevention and Research Institute of TexasUnited StatesRP120314

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-04-24
    Type: Author supporting evidence, Data collection