1CT9

CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.

Larsen, T.M., Boehlein, S.K., Schuster, S.M., Richards, N.G., Thoden, J.B., Holden, H.M., Rayment, I.

(1999) Biochemistry 38: 16146-16157

  • DOI: 10.1021/bi9915768
  • Primary Citation of Related Structures:  
    1CT9

  • PubMed Abstract: 

    • Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. Here, we describe the three-dimensional structure of the enzyme from Escherichia colidetermined and refined to 2.0 A resolution. Protein employed for this study was that of a site-directed mutant protein, Cys1Ala ...

    Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. Here, we describe the three-dimensional structure of the enzyme from Escherichia colidetermined and refined to 2.0 A resolution. Protein employed for this study was that of a site-directed mutant protein, Cys1Ala. Large crystals were grown in the presence of both glutamine and AMP. Each subunit of the dimeric protein folds into two distinct domains. The N-terminal region contains two layers of antiparallel beta-sheet with each layer containing six strands. Wedged between these layers of sheet is the active site responsible for the hydrolysis of glutamine. Key side chains employed for positioning the glutamine substrate within the binding pocket include Arg 49, Asn 74, Glu 76, and Asp 98. The C-terminal domain, responsible for the binding of both Mg(2+)ATP and aspartate, is dominated by a five-stranded parallel beta-sheet flanked on either side by alpha-helices. The AMP moiety is anchored to the protein via hydrogen bonds with O(gamma) of Ser 346 and the backbone carbonyl and amide groups of Val 272, Leu 232, and Gly 347. As observed for other amidotransferases, the two active sites are connected by a tunnel lined primarily with backbone atoms and hydrophobic and nonpolar amino acid residues. Strikingly, the three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase.

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin, Madison 53706, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARAGINE SYNTHETASE BA, B, C, D553Escherichia coliMutation(s): 1 
EC: 6.3.5.4
UniProt
Find proteins for P22106 (Escherichia coli (strain K12))
Explore P22106 
Go to UniProtKB:  P22106
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22106
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
EA [auth D],
J [auth A],
Q [auth B],
X [auth C]		ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
IUM
Query on IUM
Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
AA [auth D],
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N		 Ligand Interaction
GLN
Query on GLN
Download Ideal Coordinates CCD File 
FA [auth D],
K [auth A],
R [auth B],
Y [auth C]		GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
DA [auth D],
I [auth A],
P [auth B],
W [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.93α = 90
b = 127.1β = 90
c = 204.51γ = 90
Software Package:
Software NamePurpose
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    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