8WEX | pdb_00008wex

Crystal structure of N-acetyl sugar amidotransferase from Legionella pneumophila

• PDB DOI: https://doi.org/10.2210/pdb8WEX/pdb

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2024-05-22 
• Deposition Author(s): Gao, J., Xu, W., Ge, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: in silico

Literature

Structural Characterization of an N-Acetyl Sugar Amidotransferase Involved in the Lipopolysaccharide Biosynthesis in Bacteria.

Gao, J., Xu, W., Liu, T., Sun, W., Wang, N., Ma, J., Ge, H.

(2023) Int J Mol Sci 24

• PubMed: 37895170 
• DOI: https://doi.org/10.3390/ijms242015491
• Primary Citation Related Structures: 
  8WEX


• PubMed Abstract: 
  

  N-acetyl sugar amidotransferase (NASAT) is involved in the lipopolysaccharide (LPS) biosynthesis pathway that catalyzes the formation of the acetamido moiety (sugar-NC(=NH)CH3) on the O-chain. So far, little is known about its structural and functional properties. Here, we report the crystal structure of an N-acetyl sugar amidotransferase from Legionella pneumophila (LpNASAT) at 2.33 Å resolution. LpNASAT folds into a compact basin-shaped architecture with an unusually wide and open putative substrate-binding pocket and a conserved zinc ion-binding tetracysteine motif. The pocket contains a Rossmann-like fold with a PP-loop, suggesting that the NASAT-catalyzed amidotransfer reaction probably requires the conversion of ATP to AMP and PPi. Our data provide structural insights into the NASAT family of proteins, and allow us to possibly identify its functionally important regions.

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Organizational Affiliation: 
• Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 109.44 kDa 
• Atom Count: 6,470 
• Modeled Residue Count: 768 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl sugar amidotransferase	A, B	468	Legionella pneumophila	Mutation(s): 0  Gene Names: D1H98_00335
UniProt
Find proteins for A0A3A6V1D8 (Legionella pneumophila subsp. pneumophila) Explore A0A3A6V1D8  Go to UniProtKB:  A0A3A6V1D8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.722	α = 90
b = 74.722	β = 90
c = 319.678	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPX	data reduction
pointless	data scaling
MR-Rosetta	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Gao, J., Xu, W., Ge, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32370196
National Natural Science Foundation of China (NSFC)	China	31970103

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release