1GET

ANATOMY OF AN ENGINEERED NAD-BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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Literature

Anatomy of an engineered NAD-binding site.

Mittl, P.R.Berry, A.Scrutton, N.S.Perham, R.N.Schulz, G.E.

(1994) Protein Sci 3: 1504-1514

  • DOI: 10.1002/pro.5560030916
  • Primary Citation of Related Structures:  
    1GEU, 1GET, 1GES

  • PubMed Abstract: 
  • The coenzyme specificity of Escherichia coli glutathione reductase was switched from NADP to NAD by modifying the environment of the 2'-phosphate binding site through a set of point mutations: A179G, A183G, V197E, R198M, K199F, H200D, and R204P (Scrutton NS, Berry A, Perham RN, 1990, Nature 343:38-43) ...

    The coenzyme specificity of Escherichia coli glutathione reductase was switched from NADP to NAD by modifying the environment of the 2'-phosphate binding site through a set of point mutations: A179G, A183G, V197E, R198M, K199F, H200D, and R204P (Scrutton NS, Berry A, Perham RN, 1990, Nature 343:38-43). In order to analyze the structural changes involved, we have determined 4 high-resolution crystal structures, i.e., the structures of the wild-type enzyme (1.86 A resolution, R-factor of 16.8%), of the wild-type enzyme ligated with NADP (2.0 A, 20.8%), of the NAD-dependent mutant (1.74 A, 16.8%), and of the NAD-dependent mutant ligated with NAD (2.2 A, 16.9%). A comparison of these structures reveals subtle differences that explain details of the specificity change. In particular, a peptide rotation occurs close to the adenosine ribose, with a concomitant change of the ribose pucker. The mutations cause a contraction of the local chain fold. Furthermore, the engineered NAD-binding site assumes a less rigid structure than the NADP site of the wild-type enzyme. A superposition of the ligated structures shows a displacement of NAD versus NADP such that the electron pathway from the nicotinamide ring to FAD is elongated, which may explain the lower catalytic efficiency of the mutant. Because the nicotinamide is as much as 15 A from the sites of the mutations, this observation reminds us that mutations may have important long-range consequences that are difficult to anticipate.


    Related Citations: 
    • The Structure of Glutathione Reductase from Escherichia Coli at 1.86 Angstroms Resolution: Comparison with the Enzyme from Human Erythrocytes
      Mittl, P.R.E., Schulz, G.E.
      (1994) Protein Sci 3: 799
    • Structural Differences between Wild-Type Nad-Dependent Glutathione Reductase from Escherichia Coli and a Redesigned Nad-Dependent Mutant
      Mittl, P.R.E., Berry, A., Scrutton, N.S., Perham, R.N., Schulz, G.E.
      (1993) J Mol Biol 231: 191

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE REDUCTASEA, B450Escherichia coliMutation(s): 0 
EC: 1.6.4.2 (PDB Primary Data), 1.8.1.7 (UniProt)
UniProt
Find proteins for P06715 (Escherichia coli (strain K12))
Explore P06715 
Go to UniProtKB:  P06715
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 1 1 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.5α = 90
b = 74β = 90
c = 60.8γ = 82.5
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance