1KHZ

Structure of the ADPR-ase in complex with AMPCPR and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.

Gabelli, S.B.Bianchet, M.A.Ohnishi, Y.Ichikawa, Y.Bessman, M.J.Amzel, L.M.

(2002) Biochemistry 41: 9279-9285


  • PubMed Abstract: 
  • Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by el ...

    Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribose pyrophosphatase
A, B
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nudF (aspP, yqiE, yzzG)
EC: 3.6.1.13
Find proteins for Q93K97 (Escherichia coli (strain K12))
Go to UniProtKB:  Q93K97
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ADV
Query on ADV

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Download CCD File 
B
ALPHA-BETA METHYLENE ADP-RIBOSE
AMPCPR; {[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5-TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER
C16 H25 N5 O13 P2
ZPZRETFSCSWNDT-DBXCYWGHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.100α = 90.00
b = 67.400β = 90.00
c = 96.500γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation