6JKU | pdb_00006jku

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella Multocida

• PDB DOI: https://doi.org/10.2210/pdb6JKU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pasteurella multocida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-01 Released: 2020-03-04 
• Deposition Author(s): Manjunath, L., Bose, S., Subramanian, R.
• Funding Organization(s): Department of Biotechnology (India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida.

Manjunath, L., Coombes, D., Davies, J., Dhurandhar, M., Tiwari, V.R., Dobson, R.C.J., Sowdhamini, R., Ramaswamy, S., Bose, S.

(2020) Proteins 

• PubMed: 32865821 
• DOI: https://doi.org/10.1002/prot.25996
• Primary Citation Related Structures: 
  6JKU


• PubMed Abstract: 
  

  N-acetylglucosamine 6-phosphate deacetylase (NagA) catalyzes the conversion of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate in amino sugar catabolism. This conversion is an essential step in the catabolism of sialic acid in several pathogenic bacteria, including Pasteurella multocida, and thus NagA is identified as a potential drug target. Here, we report the unique structural features of NagA from P. multocida (PmNagA) resolved to 1.95 Å. PmNagA displays an altered quaternary architecture with unique interface interactions compared to its close homolog, the Escherichia coli NagA (EcNagA). We confirmed that the altered quaternary structure is not a crystallographic artifact using single particle electron cryo-microscopy. Analysis of the determined crystal structure reveals a set of hot-spot residues involved in novel interactions at the dimer-dimer interface. PmNagA binds to one Zn ²⁺ ion in the active site and demonstrates kinetic parameters comparable to other bacterial homologs. Kinetic studies reveal that at high substrate concentrations (~10-fold the K _M ), the tetrameric PmNagA displays hysteresis similar to its distant neighbor, the dimeric Staphylococcus aureus NagA (SaNagA). Our findings provide key information on structural and functional properties of NagA in P. multocida that could be utilized to design novel antibacterials.

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Organizational Affiliation: 
• Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India.
Manipal Academy of Higher Education, Tiger Circle, Manipal, Karnataka, India.
Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India.
Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.
Department of Biological Sciences and Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.91 kDa 
• Atom Count: 12,819 
• Modeled Residue Count: 1,529 
• Deposited Residue Count: 1,580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosamine-6-phosphate deacetylase	A, B, C, D	395	Pasteurella multocida	Mutation(s): 0  Gene Names: BGK37_09560
UniProt
Find proteins for Q9CMF5 (Pasteurella multocida (strain Pm70)) Explore Q9CMF5  Go to UniProtKB:  Q9CMF5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], PA [auth D], QA [auth D], RA [auth D], SA [auth D], U [auth B], V [auth B], W [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	DA [auth B], R [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], FA [auth C], OA [auth D], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], TA [auth D], UA [auth D], VA [auth D], WA [auth D], X [auth B], XA [auth D], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	EA [auth B], NA [auth C], S [auth A], YA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.162	α = 90
b = 139.549	β = 90
c = 166.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Manjunath, L., Bose, S., Subramanian, R.

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Funding Organization	Location	Grant Number
Department of Biotechnology (India)	India	BT/INF/22/SP22660/2017
Department of Biotechnology (India)	India	BT/PR12422/MED /31/287/214
Department of Biotechnology (India)	India	BT/PR5081/INF/156/2012
Department of Biotechnology (India)	India	BT/IN/SWEDEN/06/SR/2017-2018

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Derived calculations
• Version 1.2: 2021-03-17
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description