1OC2

The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Structure of Nadh in the Enzyme Dtdp-D-Glucose Dehydratase (Rmlb)

Beis, K.Allard, S.T.Hegeman, A.D.Murshudov, G.Philp, D.Naismith, J.H.

(2003) J Am Chem Soc 125: 11872

  • DOI: 10.1021/ja035796r
  • Primary Citation of Related Structures:  
    1OC2

  • PubMed Abstract: 
  • The structure of Streptococcus suis serotype type 2 dTDP-d-glucose 4,6-dehydratase (RmlB) has been determined to 1.5 A resolution with its nicotinamide coenzyme and substrate analogue dTDP-xylose bound in an abortive complex. During enzyme turnover, NAD(+) abstracts a hydride from the C4' atom of dTDP-glucose-forming NADH ...

    The structure of Streptococcus suis serotype type 2 dTDP-d-glucose 4,6-dehydratase (RmlB) has been determined to 1.5 A resolution with its nicotinamide coenzyme and substrate analogue dTDP-xylose bound in an abortive complex. During enzyme turnover, NAD(+) abstracts a hydride from the C4' atom of dTDP-glucose-forming NADH. After elimination of water, hydride is then transferred back to the C6' atom of dTDP-4-keto-5,6-glucosene-regenerating NAD(+). Single-crystal spectroscopic studies unambiguously show that the coenzyme has been trapped as NADH in the crystal. Electron density clearly demonstrates that in contrast to native structures of RmlB where a flat nicotinamide ring is observed, the dihydropyridine ring of the reduced cofactor in this complex is found as a boat. The si face, from which the pro-S hydride is transferred, has a concave surface. Ab initio electronic structure calculations demonstrate that the presence of an internal hydrogen bond, between the amide NH on the nicotinamide ring and one of the oxygen atoms on a phosphate group, stabilizes this distorted conformation. Additionally, calculations show that the hydride donor ability of NADH is influenced by the degree of bending in the ring and may be influenced by an active-site tyrosine residue (Tyr 161). These results demonstrate the ability of dehydratase enzymes to fine-tune the redox potential of NADH through conformational changes in the nicotinamide ring.


    Organizational Affiliation

    Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DTDP-GLUCOSE 4,6-DEHYDRATASEA, B348Streptococcus suisMutation(s): 0 
Gene Names: 
EC: 4.2.1.46
UniProt
Find proteins for Q8GIP9 (Streptococcus suis)
Explore Q8GIP9 
Go to UniProtKB:  Q8GIP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
TDX (Subject of Investigation/LOI)
Query on TDX

Download Ideal Coordinates CCD File 
C [auth A], I [auth B]THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
C15 H24 N2 O15 P2
AJUADKZRQSBUAK-KDGZBOQCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.41α = 90
b = 94.829β = 90
c = 183.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Source and taxonomy