1INI | pdb_00001ini

CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis.

Richard, S.B.Bowman, M.E.Kwiatkowski, W.Kang, I.Chow, C.Lillo, A.M.Cane, D.E.Noel, J.P.

(2001) Nat Struct Biol 8: 641-648

  • DOI: https://doi.org/10.1038/89691
  • Primary Citation Related Structures: 
    1I52, 1INI, 1INJ

  • PubMed Abstract: 

    The YgbP protein of Escherichia coli encodes the enzyme 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME) synthetase, a member of the cytidyltransferase family of enzymes. CDP-ME is an intermediate in the mevalonate-independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. Because vertebrates synthesize isoprenoid precursors using a mevalonate pathway, CDP-ME synthetase and other enzymes of the mevalonate-independent pathway for isoprenoid production represent attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. The high-resolution structures of E. coli CDP-ME synthetase in the apo form and complexed with both CTP-Mg2+ and CDP-ME-Mg2+ reveal the stereochemical principles underlying both substrate and product recognition as well as catalysis in CDP-ME synthetase. Moreover, these complexes represent the first experimental structures for any cytidyltransferase with both substrates and products bound.


  • Organizational Affiliation
    • Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 26.32 kDa 
  • Atom Count: 1,853 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE236Escherichia coli K-12Mutation(s): 0 
Gene Names: ISPD
EC: 2.7.7 (PDB Primary Data), 2.7.7.60 (UniProt)
UniProt
Find proteins for Q46893 (Escherichia coli (strain K12))
Explore Q46893 
Go to UniProtKB:  Q46893
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46893
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDM

Query on CDM



Download:Ideal Coordinates CCD File
C [auth A]4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
C14 H25 N3 O14 P2
YFAUKWZNPVBCFF-XHIBXCGHSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.99α = 90
b = 46.764β = 92.64
c = 38.387γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description