4G5H

Crystal structure of capsular polysaccharide synthesizing enzyme CapE from Staphylococcus aureus in complex with by-product

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.

Miyafusa, T., Caaveiro, J.M., Tanaka, Y., Tsumoto, K.

(2013) Febs Lett. 587: 3824-3830

  • DOI: 10.1016/j.febslet.2013.10.009

  • PubMed Abstract: 

    • CapE is an essential enzyme for the synthesis of capsular polysaccharide (CP) of pathogenic strains of Staphylococcus aureus. Herein we demonstrate that CapE is a 5-inverting 4,6-dehydratase enzyme. However, in the absence of downstream enzymes, CapE ...

    CapE is an essential enzyme for the synthesis of capsular polysaccharide (CP) of pathogenic strains of Staphylococcus aureus. Herein we demonstrate that CapE is a 5-inverting 4,6-dehydratase enzyme. However, in the absence of downstream enzymes, CapE catalyzes an additional reaction (5-back-epimerization) affording a by-product under thermodynamic control. Single-crystal X-ray crystallography was employed to identify the structure of the by-product. The structural analysis reveals a network of coordinated motions away from the active site governing the enzymatic activity of CapE. A second dynamic element (the latch) regulates the enzymatic chemoselectivity. The validity of these mechanisms was evaluated by site-directed mutagenesis.

    Organizational Affiliation: 

    Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsular polysaccharide synthesis enzyme Cap8E
A
363Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: capE
Find proteins for A0A0H3JPH0 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  A0A0H3JPH0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT
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Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP
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Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
UD7
Query on UD7
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Download CCD File 
A
[(2R,3R,4R,6R)-3-acetamido-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate
C17 H25 N3 O16 P2
XBILTLYIKDPORV-HZUXRPHDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.030α = 90.00
b = 124.030β = 90.00
c = 103.161γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
SERGUIdata collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references, Structure summary
  • Version 1.2: 2014-09-03
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description