Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.27 kDa 
• Atom Count: 4637 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 1

1NVT

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

• PDB DOI: 10.2210/pdb1NVT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-04 Released: 2003-03-25 
• Deposition Author(s): Padyana, A.K., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

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

• PubMed: 12906831 
• DOI: 10.1016/s0969-2126(03)00159-x
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate 5'-dehydrogenase	A, B	287	Methanocaldococcus jannaschii	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.65	α = 90
b = 75.62	β = 90
c = 118.79	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
MLPHARE	phasing
RESOLVE	phasing
MAID	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-04 
• Released Date: 2003-03-25 
Deposition Author(s): Padyana, A.K., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• 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