7YA2 | pdb_00007ya2

Crystal structure of capsular polysaccharide synthesis enzyme CapG from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb7YA2/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus str. Newman
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-27 Released: 2022-11-16 
• Deposition Author(s): Chen, Y., Wang, Y.C.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the capsular polysaccharide-synthesis enzyme CapG from Staphylococcus aureus.

Tien, N., Ho, C.Y., Lai, S.J., Lin, Y.C., Yang, C.S., Wang, Y.C., Huang, W.C., Chen, Y., Chang, J.J.

(2022) Acta Crystallogr F Struct Biol Commun 78: 378-385

• PubMed: 36322423 
• DOI: https://doi.org/10.1107/S2053230X22008743
• Primary Citation Related Structures: 
  7YA2


• PubMed Abstract: 
  

  Bacterial capsular polysaccharides provide protection against environmental stress and immune evasion from the host immune system, and are therefore considered to be attractive therapeutic targets for the development of anti-infectious reagents. Here, we focused on CapG, one of the key enzymes in the synthesis pathway of capsular polysaccharides type 5 (CP5) from the opportunistic pathogen Staphylococcus aureus. SaCapG catalyses the 2-epimerization of UDP-N-acetyl-D-talosamine (UDP-TalNAc) to UDP-N-acetyl-D-fucosamine (UDP-FucNAc), which is one of the nucleotide-activated precursors for the synthesis of the trisaccharide repeating units of CP5. Here, the cloning, expression and purification of recombinant SaCapG are reported. After extensive efforts, single crystals of SaCapG were successfully obtained which belonged to space group C2 and exhibited unit-cell parameters a = 302.91, b = 84.34, c = 145.09 Å, β = 110.65°. The structure was solved by molecular replacement and was refined to 3.2 Å resolution. The asymmetric unit revealed a homohexameric assembly of SaCapG, which was consistent with gel-filtration analysis. Structural comparison with UDP-N-acetyl-D-glucosamine 2-epimerase from Methanocaldococcus jannaschii identified α2, the α2-α3 loop and α10 as a gate-regulated switch controlling substrate entry and/or product release.

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Organizational Affiliation: 
• Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan.
Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
Translational Cell Therapy Center, China Medical University Hospital, Taichung, Taiwan.
Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, Taiwan.
Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 257.43 kDa 
• Atom Count: 18,050 
• Modeled Residue Count: 2,242 
• Deposited Residue Count: 2,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsular polysaccharide synthesis enzyme CapG	A, B, C, D, E, F	374	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 0  Gene Names: capG, NWMN_0101, CNH35_00585
UniProt
Find proteins for A0A0H3K5M7 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K5M7  Go to UniProtKB:  A0A0H3K5M7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 302.909	α = 90
b = 84.34	β = 110.65
c = 145.085	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Chen, Y., Wang, Y.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2311-B-241-001

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description