Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.21 kDa 
• Atom Count: 2783 
• Modelled Residue Count: 282 
• Deposited Residue Count: 284 
• Unique protein chains: 1

3ZTP

Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase

• PDB DOI: 10.2210/pdb3ZTP/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-12 Released: 2012-03-14 
• Deposition Author(s): Boissier, F., Georgescauld, F., Moynie, L., Dupuy, J.-W., Sarger, C., Podar, M., Lascu, I., Giraud, M.-F., Dautant, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.162 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

An Intersubunit Disulfide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus.

Boissier, F., Georgescauld, F., Moynie, L., Dupuy, J.W., Sarger, C., Podar, M., Lascu, I., Giraud, M.F., Dautant, A.

(2012) Proteins 80: 1658

• PubMed: 22467275 
• DOI: 10.1002/prot.24062
• Primary Citation of Related Structures:  
  3ZTO, 3ZTP, 3ZTQ, 3ZTR, 3ZTS


• PubMed Abstract: 
  

The nucleoside diphosphate kinase (Ndk) catalyzes the reversible transfer of the γ-phosphate from nucleoside triphosphate to nucleoside diphosphate. Ndks form hexamers or two types of tetramers made of the same building block, namely, the common dimer. The secondary interfaces of the Type I tetramer found in Myxococcus xanthus Ndk and of the Type II found in Escherichia coli Ndk involve the opposite sides of subunits. Up to now, the few available structures of Ndk from thermophiles were hexameric. Here, we determined the X-ray structures of four crystal forms of the Ndk from the hyperthermophilic bacterium Aquifex aeolicus (Aa-Ndk). Aa-Ndk displays numerous features of thermostable proteins and is made of the common dimer but it is a tetramer of Type I. Indeed, the insertion of three residues in a surface-exposed spiral loop, named the Kpn-loop, leads to the formation of a two-turn α-helix that prevents both hexamer and Type II tetramer assembly. Moreover, the side chain of the cysteine at position 133, which is not present in other Ndk sequences, adopts two alternate conformations. Through the secondary interface, each one forms a disulfide bridge with the equivalent Cys133 from the neighboring subunit. This disulfide bridge was progressively broken during X-ray data collection by radiation damage. Such crosslinks counterbalance the weakness of the common-dimer interface. A 40% decrease of the kinase activity at 60°C after reduction and alkylation of the protein corroborates the structural relevance of the disulfide bridge on the tetramer assembly and enzymatic function.

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Related Citations: 

• The Structure of the Escherichia Coli Nucleoside Diphosphate Kinase Reveals a New Quaternary Architecture for This Enzyme Family.
  Moynie, L., Giraud, M., Georgescauld, F., Lascu, I., Dautant, A.
  (2007) Proteins 67: 755

• Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and its Interaction with a Nucleotide Substrate at 2.0 A Resolution.
  Williams, R.L., Oren, D.A., Munoz-Dorado, J., Inouye, S., Inouye, M., Arnold, E.
  (1993) J Mol Biol 234: 1230

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Organizational Affiliation: 

Université de Bordeaux, Institut de Biochimie et de Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOSIDE DIPHOSPHATE KINASE	A, B [auth C]	142	Aquifex aeolicus	Mutation(s): 0  EC: 2.7.4.6
UniProt
Find proteins for O67528 (Aquifex aeolicus (strain VF5)) Explore O67528  Go to UniProtKB:  O67528

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.162 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.18	α = 90
b = 95.12	β = 90
c = 61.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-12 
• Released Date: 2012-03-14 
Deposition Author(s): Boissier, F., Georgescauld, F., Moynie, L., Dupuy, J.-W., Sarger, C., Podar, M., Lascu, I., Giraud, M.-F., Dautant, A.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Other