3DOO

Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis complexed with shikimate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis

Han, C.Hu, T.Wu, D.Qu, S.Zhou, J.Ding, J.Shen, X.Qu, D.Jiang, H.

(2009) FEBS J 276: 1125-1139

  • DOI: 10.1111/j.1742-4658.2008.06856.x
  • Primary Citation of Related Structures:  
    3DON, 3DOO

  • PubMed Abstract: 
  • Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate ...

    Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate. SeSDH has a k(cat) of 22.8 s(-1) and a K(m) of 73 mum towards shikimate, and a K(m) of 100 microM towards NADP. The overall folding of SeSDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211, normally regarded as important for substrate binding, does not interact with shikimate in the binary SeSDH-shikimate complex structure. However, the Y211F mutation leads to a significant decrease in k(cat) and a minor increase in the K(m) for shikimate. The results indicate that the main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SeSDH is less conserved. The usually long helix specifically recognizing the adenine ribose phosphate is substituted with a short 3(10) helix in the NADP-binding domain. Moreover, the interdomain angle of SeSDH is the widest among all known SDH structures, indicating an inactive 'open' state of the SeSDH structure. Thus, a 'closing' process might occur upon NADP binding to bring the cofactor close to the substrate for catalysis.


    Organizational Affiliation

    Institutes of Biomedical Sciences and Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Shanghai Medical College, Fudan University, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Shikimate dehydrogenaseA277Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: aroESERP1163
EC: 1.1.1.25
Find proteins for Q5HNV1 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HNV1 
Go to UniProtKB:  Q5HNV1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SKM
Query on SKM

Download Ideal Coordinates CCD File 
B [auth A](3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.189α = 90
b = 52.529β = 96.14
c = 56.777γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary