6SSG

Transaminase with DCS bound

PDB DOI: https://doi.org/10.2210/pdb6SSG/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.170
R-Value Work: 0.145
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 90.55 kDa
Atom Count: 7,425
Modelled Residue Count: 848
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ForI-DCS	A, B	424	Streptomyces kaniharaensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LUK (Subject of Investigation/LOI) Query on LUK Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	[4-[(~{Z})-[(2~{R},5~{R})-5-(azanyloxymethyl)-3,6-bis(oxidanylidene)piperazin-2-yl]methoxyiminomethyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate C₁₄ H₂₀ N₅ O₉ P HNXGFDLEQUEUAT-IZYPQUFVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]