1EQ2

THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.

Deacon, A.M.Ni, Y.S.Coleman Jr., W.G.Ealick, S.E.

(2000) Structure Fold.Des. 8: 453-462

  • Also Cited By: 3SXP

  • PubMed Abstract: 
  • ADP-L-glycero--mannoheptose 6-epimerase (AGME) is required for lipopolysaccharide (LPS) biosynthesis in most genera of pathogenic and non-pathogenic Gram-negative bacteria. It catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-gl ...

    ADP-L-glycero--mannoheptose 6-epimerase (AGME) is required for lipopolysaccharide (LPS) biosynthesis in most genera of pathogenic and non-pathogenic Gram-negative bacteria. It catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose, a precursor of the seven-carbon sugar L-glycero-mannoheptose (heptose). Heptose is an obligatory component of the LPS core domain; its absence results in a truncated LPS structure resulting in susceptibility to hydrophobic antibiotics. Heptose is not found in mammalian cells, thus its biosynthetic pathway in bacteria presents a unique target for the design of novel antimicrobial agents.


    Related Citations: 
    • Crystallization and Preliminary X-ray Diffraction Studies of the Lipopolysaccharide Core Biosynthetic Enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12
      Ding, L.,Zhang, Y.,Deacon, A.M.,Ealick, S.E.,Ni, Y.,Sun, P.,Coleman Jr., W.G.
      (1999) Acta Crystallogr.,Sect.D 55: 685


    Organizational Affiliation

    Department ofChemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
A, B, C, D, E, F, G, H, I, J
310Escherichia coli (strain K12)Gene Names: hldD (htrM, rfaD, waaD)
EC: 5.1.3.20
Find proteins for P67910 (Escherichia coli (strain K12))
Go to UniProtKB:  P67910
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
ADQ
Query on ADQ

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
C16 H25 N5 O15 P2
WFPZSXYXPSUOPY-ROYWQJLOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.460α = 90.00
b = 109.760β = 91.04
c = 181.540γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
SnBphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description