1I9A

STRUCTURAL STUDIES OF CHOLESTEROL BIOSYNTHESIS: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AND ISOPENTENYL DIPHOSPHATE ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.

Bonanno, J.B.Edo, C.Eswar, N.Pieper, U.Romanowski, M.J.Ilyin, V.Gerchman, S.E.Kycia, H.Studier, F.W.Sali, A.Burley, S.K.

(2001) Proc.Natl.Acad.Sci.USA 98: 12896-12901

  • DOI: 10.1073/pnas.181466998
  • Primary Citation of Related Structures:  1FI4

  • PubMed Abstract: 
  • X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a single-domain alpha/beta protein that catalyzes the last of thr ...

    X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a single-domain alpha/beta protein that catalyzes the last of three sequential ATP-dependent reactions which convert mevalonate to isopentenyl diphosphate. Isopentenyl disphosphate isomerase (IDI) is an alpha/beta metalloenzyme that catalyzes interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, which condense in the next step toward synthesis of sterols and a host of natural products. Homology modeling of related proteins and comparisons of the MDD and IDI structures with two other experimentally determined structures have shown that MDD is a member of the GHMP superfamily of small-molecule kinases and IDI is similar to the nudix hydrolases, which act on nucleotide diphosphatecontaining substrates. Structural models were produced for 379 proteins, encompassing a substantial fraction of both protein superfamilies. All three enzymes responsible for synthesis of isopentenyl diphosphate from mevalonate (mevalonate kinase, phosphomevalonate kinase, and MDD) share the same fold, catalyze phosphorylation of chemically similar substrates (MDD decarboxylation involves phosphorylation of mevalonate diphosphate), and seem to have evolved from a common ancestor. These structures and the structural models derived from them provide a framework for interpreting biochemical function and evolutionary relationships.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
A, B
182Escherichia coli (strain K12)Gene Names: idi (ygfV)
EC: 5.3.3.2
Find proteins for Q46822 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46822
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-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: 0.279 
  • R-Value Work: 0.229 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.758α = 90.00
b = 72.758β = 90.00
c = 204.471γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2001-03-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance