9FTC | pdb_00009ftc

Aeromonas caviae CMP-Pse5Ac7Ac synthetase in the presence of CMP-Pse5Ac7Ac.

• PDB DOI: https://doi.org/10.2210/pdb9FTC/pdb

• Classification: TRANSFERASE
• Organism(s): Aeromonas caviae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2024-10-09 
• Deposition Author(s): Cowan, A.R., Hemsworth, G.R., Keenan, T., Fascione, M.A.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 

Starting Model: experimental

Literature

Structural dissection of the CMP-pseudaminic acid synthetase, PseF.

Keenan, T., Cowan, A.R., Flack, E.K.P., Hatton, N.E., Walklett, A.J., Thomas, G.H., Hemsworth, G.R., Fascione, M.A.

(2024) Structure 32: 2399

• PubMed: 39393361 
• DOI: https://doi.org/10.1016/j.str.2024.09.017
• Primary Citation of Related Structures:  
  9FTB, 9FTC


• PubMed Abstract: 
  

  Pseudaminic acid is a non-mammalian sugar found in the surface glycoconjugates of many bacteria, including several human pathogens, and is a virulence factor thought to facilitate immune evasion. The final step in the biosynthesis of the nucleotide activated form of the sugar, CMP-Pse5Ac7Ac is performed by a CMP-Pse5Ac7Ac synthetase (PseF). Here we present the biochemical and structural characterization of PseF from Aeromonas caviae (AcPseF), with AcPseF displaying metal-dependent activity over a broad pH and temperature range. Upon binding to CMP-Pse5Ac7Ac, AcPseF undergoes dynamic movements akin to other CMP-ulosonic acid synthetases. The enzyme clearly discriminates Pse5Ac7Ac from other ulosonic acids, through active site interactions with side-chain functional groups and by positioning the molecule in a hydrophobic pocket. Finally, we show that AcPseF binds the CMP-Pse5Ac7Ac side chain in the lowest energy conformation, a trend that we observed in the structures of other enzymes of this class.

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Organizational Affiliation: 
• Department of Chemistry, University of York, York YO10 5DD, UK.
Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Department of Biology, University of York, York YO10 5DD, UK.
Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address: [e-mail].
Department of Chemistry, University of York, York YO10 5DD, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.3 kDa 
• Atom Count: 4,112 
• Modeled Residue Count: 457 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NeuA	A, B	248	Aeromonas caviae	Mutation(s): 0  Gene Names: neuA
UniProt
Find proteins for Q9R9S4 (Aeromonas caviae) Explore Q9R9S4  Go to UniProtKB:  Q9R9S4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IF6 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{R},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxane-2-carboxylic acid C22 H34 N5 O15 P XTZJKGIMUFZFBV-STPXTTIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.574	α = 90
b = 79.007	β = 92.46
c = 74.039	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Cowan, A.R., Hemsworth, G.R., Keenan, T., Fascione, M.A.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101044024

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Database references
• Version 1.2: 2024-12-18
  Changes: Database references