PDBsum entry 2vnd

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protein metals links
Hydrolase PDB id
Protein chain
207 a.a. *
Waters ×223
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The n69q mutant of vibrio cholerae endonuclease i
Structure: Endonuclease i. Chain: a. Engineered: yes. Mutation: yes. Other_details: 1 mutation \: n69q
Source: Vibrio cholerae. Organism_taxid: 666. Atcc: 14035. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: pbadgiii
1.70Å     R-factor:   0.200     R-free:   0.259
Authors: L.Niiranen,B.Altermark,B.O.Brandsdal,H.-K.S.Leiros, R.Helland,A.O.Smalas,N.P.Willassen
Key ref: L.Niiranen et al. (2008). Effects of salt on the kinetics and thermodynamic stability of endonuclease I from Vibrio salmonicida and Vibrio cholerae. FEBS J, 275, 1593-1605. PubMed id: 18312415
04-Feb-08     Release date:   12-Feb-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08038  (DRNE_VIBCH) -  Extracellular deoxyribonuclease
231 a.a.
207 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nuclease activity     1 term  


FEBS J 275:1593-1605 (2008)
PubMed id: 18312415  
Effects of salt on the kinetics and thermodynamic stability of endonuclease I from Vibrio salmonicida and Vibrio cholerae.
L.Niiranen, B.Altermark, B.O.Brandsdal, H.K.Leiros, R.Helland, A.O.Smalås, N.P.Willassen.
Adaptation to extreme environments affects the stability and catalytic efficiency of enzymes, often endowing them with great industrial potential. We compared the environmental adaptation of the secreted endonuclease I from the cold-adapted marine fish pathogen Vibrio salmonicida (VsEndA) and the human pathogen Vibrio cholerae (VcEndA). Kinetic analysis showed that VsEndA displayed unique halotolerance. It retained a considerable amount of activity from low concentrations to at least 0.6 m NaCl, and was adapted to work at higher salt concentrations than VcEndA by maintaining a low K(m) value and increasing k(cat). In differential scanning calorimetry, salt stabilized both enzymes, but the effect on the calorimetric enthalpy and cooperativity of unfolding was larger for VsEndA, indicating salt dependence. Mutation of DNA binding site residues (VsEndA, Q69N and K71N; VcEndA, N69Q and N71K) affected the kinetic parameters. The VsEndA Q69N mutation also increased the T(m) value, whereas other mutations affected mainly DeltaH(cal). The determined crystal structure of VcEndA N69Q revealed the loss of one hydrogen bond present in native VcEndA, but also the formation of a new hydrogen bond involving residue 69 that could possibly explain the similar T(m) values for native and N69Q-mutated VcEndA. Structural analysis suggested that the stability, catalytic efficiency and salt tolerance of EndA were controlled by small changes in the hydrogen bonding networks and surface electrostatic potential. Our results indicate that endonuclease I adaptation is closely coupled to the conditions of the habitats of natural Vibrio, with VsEndA displaying a remarkable salt tolerance unique amongst the endonucleases characterized so far.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21510974 M.K.Purohit, and S.P.Singh (2011).
Comparative analysis of enzymatic stability and amino acid sequences of thermostable alkaline proteases from two haloalkaliphilic bacteria isolated from Coastal region of Gujarat, India.
  Int J Biol Macromol, 49, 103-112.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20640228 M.O.Fenley, M.Mascagni, J.McClain, A.R.Silalahi, and N.A.Simonov (2010).
Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration.
  J Chem Theory Comput, 6, 300-314.  
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