1V4A | pdb_00001v4a

Structure of the N-terminal Domain of Escherichia coli Glutamine Synthetase adenylyltransferase

• PDB DOI: https://doi.org/10.2210/pdb1V4A/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-12 Released: 2004-07-27 
• Deposition Author(s): Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Ollis, D.L., Vasudevan, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure of the n-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase

Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Huber, T., Vasudevan, S.G., Ollis, D.L.

(2004) Structure 12: 861-869

• PubMed: 15130478 
• DOI: https://doi.org/10.1016/j.str.2004.02.029
• Primary Citation Related Structures: 
  1V4A


• PubMed Abstract: 
  

  We report the crystal structure of the N-terminal domain of Escherichia coli adenylyltransferase that catalyzes the reversible nucleotidylation of glutamine synthetase (GS), a key enzyme in nitrogen assimilation. This domain (AT-N440) catalyzes the deadenylylation and subsequent activation of GS. The structure has been divided into three subdomains, two of which bear some similarity to kanamycin nucleotidyltransferase (KNT). However, the orientation of the two domains in AT-N440 differs from that in KNT. The active site of AT-N440 has been identified on the basis of structural comparisons with KNT, DNA polymerase beta, and polyadenylate polymerase. AT-N440 has a cluster of metal binding residues that are conserved in polbeta-like nucleotidyl transferases. The location of residues conserved in all ATase sequences was found to cluster around the active site. Many of these residues are very likely to play a role in catalysis, substrate binding, or effector binding.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, James Cook University, Townsville, Queensland 4811, Australia. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.04 kDa 
• Atom Count: 3,541 
• Modeled Residue Count: 429 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-ammonia-ligase adenylyltransferase	A	440	Escherichia coli	Mutation(s): 13  EC: 2.7.7.42 (PDB Primary Data), 2.7.7.89 (UniProt)
UniProt
Find proteins for P30870 (Escherichia coli (strain K12)) Explore P30870  Go to UniProtKB:  P30870

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.269 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.836	α = 90
b = 116.836	β = 90
c = 67.744	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Ollis, D.L., Vasudevan, S.G.

Revision History  

• Version 1.0: 2004-07-27
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Structure summary