4G5H | pdb_00004g5h

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

• PDB DOI: https://doi.org/10.2210/pdb4G5H/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-18 Released: 2013-08-28 
• Deposition Author(s): Miyafusa, T., Caaveiro, J.M.M., Tanaka, Y., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

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

• PubMed: 24157361 
• DOI: https://doi.org/10.1016/j.febslet.2013.10.009
• Primary Citation of Related Structures:  
  4G5H


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.55 kDa 
• Atom Count: 3,104 
• Modelled Residue Count: 346 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsular polysaccharide synthesis enzyme Cap8E	A	363	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: capE EC: 4.2.1.115 (PDB Primary Data), 5.1.3.2 (UniProt)
UniProt
Find proteins for A0A0H3JPH0 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JPH0  Go to UniProtKB:  A0A0H3JPH0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
UD7	C [auth A], D [auth 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
FMT	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.03	α = 90
b = 124.03	β = 90
c = 103.161	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Miyafusa, T., Caaveiro, J.M.M., Tanaka, Y., Tsumoto, K.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references, Structure summary
• Version 1.2: 2014-09-03
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Derived calculations