5Z8B | pdb_00005z8b

Truncated N-acetylglucosaminyl transferase KfiA from E. coli K5 strain apo form

• PDB DOI: https://doi.org/10.2210/pdb5Z8B/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2018-01-31 Released: 2019-02-06 
• Deposition Author(s): Hori, H., Kakuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structural and functional analysis of KfiA, a UDP-GlcNAc transferase involved in Escherichia coli K5 heparosan biosynthesis.

Maeda, K., Sakamoto, A., Matsuura, K., Toyoda, K., Hori, H., Onishi, M., Baba, Y., Kawaguchi, Y., Ishibashi, Y., Okino, N., Nishimoto, E., Sugiura, N., Teramoto, T., Kakuta, Y.

(2026) Carbohydr Res 570: 110123-110123

• PubMed: 42854325 
• DOI: https://doi.org/10.1016/j.carres.2026.110123
• Primary Citation Related Structures: 
  27ON, 5Z8B


• PubMed Abstract: 
  

  Heparosan is a linear glycosaminoglycan-related polysaccharide produced as the capsular polysaccharide of Escherichia coli K5. Its biosynthesis requires alternating transfer of N-acetylglucosamine and glucuronic acid by the glycosyltransferases KfiA and KfiC, respectively, but the structural basis of KfiA function has remained unclear. Here, we determined crystal structures of a C-terminally truncated KfiA in the apo state and in complex with UDP and a metal ion tentatively assigned as Mn ²⁺ , and combined structural analysis with functional characterization. KfiA adopts a conserved GT-A fold with a well-defined nucleotide- and metal-binding center. Structural and biochemical analyses further distinguish the core donor-associated catalytic region from peripheral structural elements that contribute to efficient glycosyl transfer. Comparison with related glycosyltransferases reveals a conserved structural framework for UDP-GlcNAc utilization. These results provide a structural basis for understanding KfiA function and heparosan chain extension in the two-enzyme KfiA-KfiC system.

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Organizational Affiliation: 
• Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
Laboratory of Marine Resource Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
Institute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.55 kDa 
• Atom Count: 3,376 
• Modeled Residue Count: 413 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KfiA protein	A, B	242	Escherichia coli	Mutation(s): 0  Gene Names:  KfiA, kfiA, A4T40_20310, A9X62_20115, APT94_25675, CCL28_04130, CT143_12180, CT144_09435, CUB98_02030, CUB99_17445, SM09_03227
UniProt
Find proteins for Q47332 (Escherichia coli) Explore Q47332  Go to UniProtKB:  Q47332

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.409	α = 90
b = 70.862	β = 90
c = 147.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Hori, H., Kakuta, Y.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references
• Version 1.2: 2026-10-28
  Changes: Database references, Structure summary