1O9B

QUINATE/SHIKIMATE DEHYDROGENASE YDIB COMPLEXED WITH NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Shikimate Dehydrogenase Aroe and its Paralog Ydib: A Common Structural Framework for Different Activities

Michel, G.Roszak, A.W.Sauve, V.Mclean, J.Matte, A.Coggins, J.R.Cygler, M.Lapthorn, A.J.

(2003) J.Biol.Chem. 278: 19463

  • DOI: 10.1074/jbc.M300794200
  • Primary Citation of Related Structures:  1NYT

  • PubMed Abstract: 
  • Shikimate dehydrogenase catalyzes the fourth step of the shikimate pathway, the essential route for the biosynthesis of aromatic compounds in plants and microorganisms. Absent in metazoans, this pathway is an attractive target for nontoxic herbicides ...

    Shikimate dehydrogenase catalyzes the fourth step of the shikimate pathway, the essential route for the biosynthesis of aromatic compounds in plants and microorganisms. Absent in metazoans, this pathway is an attractive target for nontoxic herbicides and drugs. Escherichia coli expresses two shikimate dehydrogenase paralogs, the NADP-specific AroE and a putative enzyme YdiB. Here we characterize YdiB as a dual specificity quinate/shikimate dehydrogenase that utilizes either NAD or NADP as a cofactor. Structures of AroE and YdiB with bound cofactors were determined at 1.5 and 2.5 A resolution, respectively. Both enzymes display a similar architecture with two alpha/beta domains separated by a wide cleft. Comparison of their dinucleotide-binding domains reveals the molecular basis for cofactor specificity. Independent molecules display conformational flexibility suggesting that a switch between open and closed conformations occurs upon substrate binding. Sequence analysis and structural comparison led us to propose the catalytic machinery and a model for 3-dehydroshikimate recognition. Furthermore, we discuss the evolutionary and metabolic implications of the presence of two shikimate dehydrogenases in E. coli and other organisms.


    Organizational Affiliation

    Biotechnology Research Institute, NRC Macromolecular Structure Group, Montreal, Quebec H4P 2R2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN YDIB
A, B
288Escherichia coli (strain K12)Gene Names: ydiB
EC: 1.1.1.282
Find proteins for P0A6D5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6D5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 157.874α = 90.00
b = 157.874β = 90.00
c = 40.011γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-12-12 
  • Released Date: 2003-02-01 
  • Deposition Author(s): Michel, G., Cygler, M.

Revision History 

  • Version 1.0: 2003-02-01
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance