12AS | pdb_000012as

ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE AND AMP

• PDB DOI: https://doi.org/10.2210/pdb12AS/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-12-02 Released: 1998-12-30 
• Deposition Author(s): Nakatsu, T., Kato, H., Oda, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.287 (Depositor) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.

Nakatsu, T., Kato, H., Oda, J.

(1998) Nat Struct Biol 5: 15-19

• PubMed: 9437423 
• DOI: https://doi.org/10.1038/nsb0198-15
• Primary Citation Related Structures: 
  11AS, 12AS


• PubMed Abstract: 
  

  The crystal structure of E. coli asparagine synthetase has been determined by X-ray diffraction analysis at 2.5 A resolution. The overall structure of the enzyme is remarkably similar to that of the catalytic domain of yeast aspartyl-tRNA synthetase despite low sequence similarity. These enzymes have a common reaction mechanism that implies the formation of an aminoacyl-adenylate intermediate. The active site architecture and most of the catalytic residues are also conserved in both enzymes. These proteins have probably evolved from a common ancestor even though their sequence similarities are small. The functional and structural similarities of both enzymes suggest that new enzymatic activities would generally follow the recruitment of a protein catalyzing a similar chemical reaction.

---

Organizational Affiliation: 
• Institute for Chemical Research, Kyoto University, Japan. [e-mail]

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: 74.23 kDa 
• Atom Count: 5,385 
• Modeled Residue Count: 654 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARAGINE SYNTHETASE	A, B	330	Escherichia coli K-12	Mutation(s): 2  Gene Names: ASNA EC: 6.3.1.1
UniProt
Find proteins for P00963 (Escherichia coli (strain K12)) Explore P00963  Go to UniProtKB:  P00963

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ASN	C [auth A], E [auth B]	ASPARAGINE C4 H8 N2 O3 DCXYFEDJOCDNAF-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.287 (Depositor) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53	α = 90
b = 126.13	β = 105.59
c = 52.86	γ = 90

Software Package:

Software Name	Purpose
PROCESS	data collection
PROCESS	data reduction
X-PLOR	model building
X-PLOR	refinement
PROCESS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-30 
Deposition Author(s): Nakatsu, T., Kato, H., Oda, J.

Revision History  

• Version 1.0: 1998-12-30
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2023-08-02
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection