3D4J

Crystal structure of Human mevalonate diphosphate decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure.

Voynova, N.E.Fu, Z.Battaile, K.P.Herdendorf, T.J.Kim, J.J.Miziorko, H.M.

(2008) Arch Biochem Biophys 480: 58-67

  • DOI: https://doi.org/10.1016/j.abb.2008.08.024
  • Primary Citation of Related Structures:  
    3D4J

  • PubMed Abstract: 

    Expression in Escherichia coli of his-tagged human mevalonate diphosphate decarboxylase (hMDD) has expedited enzyme isolation, characterization, functional investigation of the mevalonate diphosphate binding site, and crystal structure determination (2.4A resolution). hMDD exhibits V(max)=6.1+/-0.5 U/mg; K(m) for ATP is 0.69+/-0.07 mM and K(m) for (R,S) mevalonate diphosphate is 28.9+/-3.3 microM. Conserved polar residues predicted to be in the hMDD active site were mutated to test functional importance. R161Q exhibits a approximately 1000-fold diminution in specific activity, while binding the fluorescent substrate analog, TNP-ATP, comparably to wild-type enzyme. Diphosphoglycolyl proline (K(i)=2.3+/-0.3 uM) and 6-fluoromevalonate 5-diphosphate (K(i)=62+/-5 nM) are competitive inhibitors with respect to mevalonate diphosphate. N17A exhibits a V(max)=0.25+/-0.0 2U/mg and a 15-fold inflation in K(m) for mevalonate diphosphate. N17A's K(i) values for diphosphoglycolyl proline and fluoromevalonate diphosphate are inflated (>70-fold and 40-fold, respectively) in comparison with wild-type enzyme. hMDD structure indicates the proximity (2.8A) between R161 and N17, which are located in an interior pocket of the active site cleft. The data suggest the functional importance of R161 and N17 in the binding and orientation of mevalonate diphosphate.


  • Organizational Affiliation

    Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphosphomevalonate decarboxylase
A, B
400Homo sapiensMutation(s): 0 
Gene Names: MVDMPD
EC: 4.1.1.33
UniProt & NIH Common Fund Data Resources
Find proteins for P53602 (Homo sapiens)
Explore P53602 
Go to UniProtKB:  P53602
PHAROS:  P53602
GTEx:  ENSG00000167508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53602
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.96α = 90
b = 53.19β = 107.25
c = 97.79γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description