7P7I

Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides

• PDB DOI: https://doi.org/10.2210/pdb7P7I/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, Plesiomonas shigelloides 302-73
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-19 Released: 2022-07-27 
• Deposition Author(s): Roy, S., Isupov, M.N., Harmer, N.J., Ames, J.R.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.183 

Literature

Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases

Cross, A.R., Roy, S., Vivoli Vega, M., Rejzek, M., Nepogodiev, S.A., Cliff, M., Salmon, D., Isupov, M.N., Field, R.A., Prior, J.L., Harmer, N.J.

(2022) J Biol Chem 

• DOI: https://doi.org/10.1016/j.jbc.2022.101903

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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 93.32 kDa 
• Atom Count: 5,488 
• Modelled Residue Count: 609 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase	A [auth AAA], B [auth BBB]	417	Saccharomyces cerevisiae S288C, Plesiomonas shigelloides 302-73 This entity is chimeric	Mutation(s): 0  Gene Names: SMT3, YDR510W, D9719.15, nagK, PLESHI_11010 EC: 2.7.1.59
UniProt
Find proteins for R8APY9 (Plesiomonas shigelloides 302-73) Explore R8APY9  Go to UniProtKB:  R8APY9
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306
UniProt Groups	R8APY9Q12306

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth AAA], O [auth BBB]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	E [auth AAA]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	C [auth AAA], D [auth AAA], M [auth BBB]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	F [auth AAA], N [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	L [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.183 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.23	α = 90
b = 95.23	β = 90
c = 180.55	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
DM	model building
BUSTER	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Roy, S., Isupov, M.N., Harmer, N.J., Ames, J.R.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N001591/1

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Database references
• Version 1.2: 2023-02-15
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-02-07
  Changes: Refinement description