4XRR

Crystal structure of cals8 from micromonospora echinospora (P294S mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural Characterization of CalS8, a TDP-alpha-D-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis.

Singh, S.Michalska, K.Bigelow, L.Endres, M.Kharel, M.K.Babnigg, G.Yennamalli, R.M.Bingman, C.A.Joachimiak, A.Thorson, J.S.Phillips, G.N.

(2015) J. Biol. Chem. 290: 26249-26258

  • DOI: 10.1074/jbc.M115.673459

  • PubMed Abstract: 
  • Classical UDP-glucose 6-dehydrogenases (UGDHs; EC 1.1.1.22) catalyze the conversion of UDP-α-d-glucose (UDP-Glc) to the key metabolic precursor UDP-α-d-glucuronic acid (UDP-GlcA) and display specificity for UDP-Glc. The fundamental biochemical and st ...

    Classical UDP-glucose 6-dehydrogenases (UGDHs; EC 1.1.1.22) catalyze the conversion of UDP-α-d-glucose (UDP-Glc) to the key metabolic precursor UDP-α-d-glucuronic acid (UDP-GlcA) and display specificity for UDP-Glc. The fundamental biochemical and structural study of the UGDH homolog CalS8 encoded by the calicheamicin biosynthetic gene is reported and represents one of the first studies of a UGDH homolog involved in secondary metabolism. The corresponding biochemical characterization of CalS8 reveals CalS8 as one of the first characterized base-permissive UGDH homologs with a >15-fold preference for TDP-Glc over UDP-Glc. The corresponding structure elucidations of apo-CalS8 and the CalS8·substrate·cofactor ternary complex (at 2.47 and 1.95 Å resolution, respectively) highlight a notably high degree of conservation between CalS8 and classical UGDHs where structural divergence within the intersubunit loop structure likely contributes to the CalS8 base permissivity. As such, this study begins to provide a putative blueprint for base specificity among sugar nucleotide-dependent dehydrogenases and, in conjunction with prior studies on the base specificity of the calicheamicin aminopentosyltransferase CalG4, provides growing support for the calicheamicin aminopentose pathway as a TDP-sugar-dependent process.


    Organizational Affiliation

    From the Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536-0596.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CalS8
A, B
456Micromonospora echinosporaMutation(s): 1 
Gene Names: calS8
Find proteins for Q8KNF6 (Micromonospora echinospora)
Go to UniProtKB:  Q8KNF6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 2.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.392α = 90.00
b = 88.200β = 103.41
c = 70.936γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXmodel building
HKL-3000data scaling
HKL-3000data reduction
MR-Rosettaphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 2.0: 2017-11-08
    Type: Database references, Derived calculations, Polymer sequence, Source and taxonomy