1NVT | pdb_00001nvt

Crystal structure of Shikimate Dehydrogenase (AROE or MJ1084) in complex with NADP+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.260 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

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Literature

Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution

Padyana, A.K., Burley, S.K.

(2003) Structure 11: 1005-1013

  • DOI: https://doi.org/10.1016/s0969-2126(03)00159-x
  • Primary Citation Related Structures: 
    1NVT

  • PubMed Abstract: 

    The crystal structure of Methanococcus jannaschii shikimate 5-dehydrogenase (MjSDH) bound to the cofactor nicotinamide adenine dinucleotide phosphate (NADP) has been determined at 2.35 A resolution. Shikimate 5-dehydrogenase (SDH) is responsible for NADP-dependent catalysis of the fourth step in shikimate biosynthesis, which is essential for aromatic amino acid metabolism in bacteria, microbial eukaryotes, and plants. The structure of MjSDH is a compact alpha/beta sandwich with two distinct domains, responsible for binding substrate and the NADP cofactor, respectively. A phylogenetically conserved deep cleft on the protein surface corresponds to the enzyme active site. The structure reveals a topologically new domain fold within the N-terminal segment of the polypeptide chain, which binds substrate and supports dimerization. Insights gained from homology modeling and sequence/structure comparisons suggest that the SDHs represent a unique class of dehydrogenases. The structure provides a framework for further investigation to discover and develop novel inhibitors targeting this essential enzyme.

    • Organizational Affiliation: 
    • Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 64.27 kDa 
  • Atom Count: 4,637 
  • Modeled Residue Count: 574 
  • Deposited Residue Count: 574 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Shikimate 5'-dehydrogenase
A, B
287Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: aroE
EC: 1.1.1.25
UniProt
Find proteins for Q58484 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58484 
Go to UniProtKB:  Q58484
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58484
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.260 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.65α = 90
b = 75.62β = 90
c = 118.79γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
RESOLVEphasing
MAIDphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references