4ZTC | pdb_00004ztc

PglE Aminotransferase in complex with External Aldimine, Mutant K184A

• PDB DOI: https://doi.org/10.2210/pdb4ZTC/pdb

• Classification: TRANSFERASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-05-14 Released: 2015-07-29 
• Deposition Author(s): Riegert, A.S., Thoden, J.B., Young, N.M., Watson, D.C., Holden, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure of the external aldimine form of PglE, an aminotransferase required for N,N'-diacetylbacillosamine biosynthesis.

Riegert, A.S., Young, N.M., Watson, D.C., Thoden, J.B., Holden, H.M.

(2015) Protein Sci 24: 1609-1616

• PubMed: 26178292 
• DOI: https://doi.org/10.1002/pro.2745
• Primary Citation Related Structures: 
  4ZTC


• PubMed Abstract: 
  

  N,N'-diacetylbacillosamine is a novel sugar that plays a key role in bacterial glycosylation. Three enzymes are required for its biosynthesis in Campylobacter jejuni starting from UDP-GlcNAc. The focus of this investigation, PglE, catalyzes the second step in the pathway. It is a PLP-dependent aminotransferase that converts UDP-2-acetamido-4-keto-2,4,6-trideoxy-d-glucose to UDP-2-acetamido-4-amino-2,4,6-trideoxy-d-glucose. For this investigation, the structure of PglE in complex with an external aldimine was determined to a nominal resolution of 2.0 Å. A comparison of its structure with those of other sugar aminotransferases reveals a remarkable difference in the manner by which PglE accommodates its nucleotide-linked sugar substrate.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706.
Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada, K1A OR6.

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)

Macromolecule Content 

• Total Structure Weight: 44.62 kDa 
• Atom Count: 3,416 
• Modeled Residue Count: 385 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase homolog	A	386	Campylobacter jejuni	Mutation(s): 1  EC: 2.6.1.34
UniProt
Find proteins for Q0P9D3 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9D3  Go to UniProtKB:  Q0P9D3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RA	B [auth A]	[(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate C25 H36 N5 O20 P3 BKHPSAUTHKIVAK-OTBUILFPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.161	α = 90
b = 66.161	β = 90
c = 169.013	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Riegert, A.S., Thoden, J.B., Young, N.M., Watson, D.C., Holden, H.M.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description