8Y97 | pdb_00008y97

Crystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006, PMP-bound form

• PDB DOI: https://doi.org/10.2210/pdb8Y97/pdb

• Classification: TRANSFERASE
• Organism(s): Prodigiosinella confusarubida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-06 Released: 2024-12-18 
• Deposition Author(s): Pramono, H., Yoshida, A., Nishiyama, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.257 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel heterooligomeric aminotransferase from Serratia sp. ATCC 39006 provides insights into function.

Pramono, H., Yoshida, A., Hirashima, Y., Sone, Y., Terada, T., Kosono, S., Nishiyama, M.

(2025) FEBS Lett 599: 74-88

• PubMed: 39618122 
• DOI: https://doi.org/10.1002/1873-3468.15068
• Primary Citation Related Structures: 
  8Y96, 8Y97, 8Y98


• PubMed Abstract: 
  

  Serratia sp. ATCC 39006 has two tandemly positioned genes, ser4 and ser5, both annotated as sugar aminotransferases, in a putative secondary metabolite biosynthetic gene cluster. Ser5 possesses a complete fold-type I aminotransferase fold, while Ser4 lacks the N- and C-terminal regions and a catalytically important lysine residue of fold-type I aminotransferase. We herein revealed that Ser4 and Ser5 formed a heterotetrameric complex (SerTA) with aminotransferase activity and determined the crystal structures. MD simulations and activity assays with SerTA variants indicated that residues from helix α-8* of inactive Ser4 are important for activity, confirming the importance of heterocomplex formation for activity. Furthermore, the structures suggest that SerTA recognizes a substrate loaded on the carrier protein.

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Organizational Affiliation: 
• Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 149.54 kDa 
• Atom Count: 9,733 
• Modeled Residue Count: 1,234 
• Deposited Residue Count: 1,322 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegT/DnrJ/EryC1/StrS family aminotransferase	A, C [auth B]	443	Prodigiosinella confusarubida	Mutation(s): 0  Gene Names: CWC46_09295, Ser39006_009300
UniProt
Find proteins for A0A2I5TIB4 (Serratia sp. (strain ATCC 39006)) Explore A0A2I5TIB4  Go to UniProtKB:  A0A2I5TIB4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DegT/DnrJ/EryC1/StrS aminotransferase	B [auth C], D	218	Prodigiosinella confusarubida	Mutation(s): 0  Gene Names: CWC46_09290, Ser39006_009295
UniProt
Find proteins for A0A2I5T5Y7 (Serratia sp. (strain ATCC 39006)) Explore A0A2I5T5Y7  Go to UniProtKB:  A0A2I5T5Y7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP (Subject of Investigation/LOI)	E [auth A], F [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.257 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.465	α = 90
b = 180.934	β = 90
c = 183.306	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Pramono, H., Yoshida, A., Nishiyama, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17H06168
Japan Society for the Promotion of Science (JSPS)	Japan	22H00355

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references