8Y96 | pdb_00008y96

Crystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/1873-3468.15068
  • Primary Citation of 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.


  • Organizational Affiliation

    Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DegT/DnrJ/EryC1/StrS family aminotransferaseA,
C [auth B]
443Prodigiosinella confusarubidaMutation(s): 0 
Gene Names: CWC46_09295Ser39006_009300
UniProt
Find proteins for A0A2I5TIB4 (Serratia sp. (strain ATCC 39006))
Explore A0A2I5TIB4 
Go to UniProtKB:  A0A2I5TIB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I5TIB4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DegT/DnrJ/EryC1/StrS aminotransferaseB [auth C],
D
218Prodigiosinella confusarubidaMutation(s): 0 
Gene Names: CWC46_09290Ser39006_009295
UniProt
Find proteins for A0A2I5T5Y7 (Serratia sp. (strain ATCC 39006))
Explore A0A2I5T5Y7 
Go to UniProtKB:  A0A2I5T5Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I5T5Y7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.688α = 90
b = 181.029β = 90
c = 182.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17H06168
Japan Society for the Promotion of Science (JSPS)Japan22H00355

Revision History  (Full details and data files)

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