6SSE

Transaminase with PMP bound

• PDB DOI: https://doi.org/10.2210/pdb6SSE/pdb

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


• Deposited: 2019-09-06 Released: 2020-01-15 
• Deposition Author(s): Naismith, J.H., Gao, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.

Gao, S., Liu, H., de Crecy-Lagard, V., Zhu, W., Richards, N.G.J., Naismith, J.H.

(2019) Chem Commun (Camb) 55: 14502-14505

• PubMed: 31730149 
• DOI: https://doi.org/10.1039/c9cc06975e
• Primary Citation of Related Structures:  
  6SSD, 6SSE, 6SSF, 6SSG


• PubMed Abstract: 
  

  ForI is a PLP-dependent enzyme from the biosynthetic pathway of the C-nucleoside antibiotic formycin. Cycloserine is thought to inhibit PLP-dependent enzymes by irreversibly forming a PMP-isoxazole. We now report that ForI forms novel PMP-diketopiperazine derivatives following incubation with both d and l cycloserine. This unexpected result suggests chemical diversity in the chemistry of cycloserine inhibition.

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Organizational Affiliation: 

Research Complex at Harwell, Didcot, OX11 0FA, UK.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 90.09 kDa 
• Atom Count: 7,445 
• Modelled Residue Count: 848 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ForI-PMP	A, B	424	Streptomyces kaniharaensis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP (Subject of Investigation/LOI)	C [auth A], G [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.264	α = 90
b = 125.828	β = 90
c = 142.747	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Naismith, J.H., Gao, S.

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release