1QAE

THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The active site of Serratia endonuclease contains a conserved magnesium-water cluster.

Miller, M.D.Cai, J.Krause, K.L.

(1999) J.Mol.Biol. 288: 975-988

  • DOI: 10.1006/jmbi.1999.2729

  • PubMed Abstract: 
  • Serratia endonuclease is an important member of a class of magnesium dependent nucleases that are widely distributed in nature. Here, we describe the location and geometry of a magnesium-water cluster within the active site of this enzyme. The sole p ...

    Serratia endonuclease is an important member of a class of magnesium dependent nucleases that are widely distributed in nature. Here, we describe the location and geometry of a magnesium-water cluster within the active site of this enzyme. The sole protein ligand of the magnesium atom is Asn119; this metal ion is also associated with five water molecules to complete an octahedral coordination complex. These water molecules are very well ordered and there is no evidence of rotational disorder or motion. Glu127 and His89 are located nearby and each is hydrogen bonded to water molecules in the coordination sphere. Asp86 is not chelated to the magnesium or its surrounding water molecules. Results of kinetics and site-specific mutagenesis experiments suggest that this metal-water cluster contains the catalytic metal ion of this enzyme. All residues which hydrogen bond to the water molecules that coordinate the magnesium atom are conserved in nucleases homologous to Serratia endonuclease, suggesting that the water cluster is a conserved feature of this family of enzymes. We offer a detailed structural comparison to one other nuclease, the homing endonuclease I-PpoI, that has recently been shown, in spite of a lack of sequence homology, to share a similar active site geometry to Serratia endonuclease. Evidence from both of these structures suggests that the magnesium of Serratia nuclease participates in catalysis via an inner sphere mechanism.


    Related Citations: 
    • 2.1 Angstroms Structure of Serratia Endonuclease Suggests a Mechanism for Binding to Double-Stranded DNA
      Miller, M.D.,Tanner, J.,Alpaugh, M.,Benedik, M.J.,Krause, K.L.
      (1994) Nat.Struct.Mol.Biol. 1: 461
    • Identification of the Serratia Endonuclease Dimer: Structural Basis and Implications for Catalysis
      Miller, M.D.,Krause, K.L.
      (1996) Protein Sci. 5: 24


    Organizational Affiliation

    Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5934, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (EXTRACELLULAR ENDONUCLEASE)
A, B
245Serratia marcescensMutation(s): 0 
Gene Names: nucA (nuc)
EC: 3.1.30.2
Find proteins for P13717 (Serratia marcescens)
Go to UniProtKB:  P13717
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.700α = 90.00
b = 74.500β = 90.00
c = 68.900γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MADNESSdata reduction
X-PLORmodel building
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling
ARP/wARPmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-04-18
    Type: Data collection