9GAF

PRECURSOR OF THE W11F MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM

• PDB DOI: https://doi.org/10.2210/pdb9GAF/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Elizabethkingia meningoseptica
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Structural insights into the mechanism of intramolecular proteolysis.

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

(1999) Cell 98: 651-661

• PubMed: 10490104 
• DOI: https://doi.org/10.1016/s0092-8674(00)80052-5
• Primary Citation of Related Structures:  
  9GAA, 9GAC, 9GAF


• 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 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.

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Organizational Affiliation: 

Department of Biophysics, Boston University School of Medicine, Massachusetts 02118-2526, 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: 64.43 kDa 
• Atom Count: 4,680 
• Modelled Residue Count: 582 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GLYCOSYLASPARAGINASE)	A, B [auth C]	295	Elizabethkingia meningoseptica	Mutation(s): 1  EC: 3.5.1.26
UniProt
Find proteins for Q47898 (Elizabethkingia miricola) Explore Q47898  Go to UniProtKB:  Q47898

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLY	C [auth A], D [auth C]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.3	α = 80.8
b = 52.8	β = 90.5
c = 62.4	γ = 105.1

Software Package:

Software Name	Purpose
XTALVIEW	refinement
MLPHARE	phasing
DM	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• 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: Advisory, Database references
• Version 1.4: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description