3ZTP

Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE KINASEA,
B [auth C]
142Aquifex aeolicusMutation(s): 0 
EC: 2.7.4.6
UniProt
Find proteins for O67528 (Aquifex aeolicus (strain VF5))
Explore O67528 
Go to UniProtKB:  O67528
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67528
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 = 52.18α = 90
b = 95.12β = 90
c = 61.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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