9GAC

PRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the mechanism of intramolecular proteolysis.

Xu, Q.Buckley, D.Guan, C.Guo, H.C.

(1999) Cell 98: 651-661

  • DOI: 10.1016/s0092-8674(00)80052-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A variety of proteins, including glycosylasparaginase, have recently been found to activate functions by self-catalyzed peptide bond rearrangements from single-chain precursors. Here we present the 1.9 A crystal structures of glycosylasparaginase pre ...

    A variety of proteins, including glycosylasparaginase, have recently been found to activate functions by self-catalyzed peptide bond rearrangements from single-chain precursors. Here we present the 1.9 A crystal structures of glycosylasparaginase precursors that are able to autoproteolyze via an N --> O acyl shift. Several conserved residues are aligned around the scissile peptide bond that is in a highly strained trans peptide bond configuration. The structure illustrates how a nucleophilic side chain may attack the scissile peptide bond at the immediate upstream backbone carbonyl and provides an understanding of the structural basis for peptide bond cleavage via an N --> O or N --> S acyl shift that is used by various groups of intramolecular autoprocessing proteins.


    Organizational Affiliation

    Department of Biophysics, Boston University School of Medicine, Massachusetts 02118-2526, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLYCOSYLASPARAGINASE)
A, C
295Elizabethkingia meningosepticaMutation(s): 1 
EC: 3.5.1.26
Find proteins for Q47898 (Elizabethkingia miricola)
Go to UniProtKB:  Q47898
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download CCD File 
A, C
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.3α = 80.8
b = 52.8β = 90.5
c = 62.4γ = 105.1
Software Package:
Software NamePurpose
XTALVIEWrefinement
MLPHAREphasing
DMmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1999-06-15 
  • Released Date: 2000-06-16 
  • Deposition Author(s): Guo, H.-C., Xu, Q.

Revision History 

  • Version 1.0: 2000-06-16
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-14
    Changes: Database references