8AOZ | pdb_00008aoz

ForT Mutant L24A

PDB DOI: https://doi.org/10.2210/pdb8AOZ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Streptomyces kaniharaensis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2022-08-09 Released: 2022-09-07
Deposition Author(s): Li, W., Naismith, J.H.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.232 (Depositor), 0.205 (DCC)
R-Value Work:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase.

Li, W., Girt, G.C., Radadiya, A., Stewart, J.J.P., Richards, N.G.J., Naismith, J.H.

(2023) Open Biol 13: 220287-220287

PubMed: 36629016 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1098/rsob.220287
Primary Citation Related Structures:
8AOZ, 8AP0

PubMed Abstract:
The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1 H -pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.

Organizational Affiliation

Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK.

Macromolecule Content

Total Structure Weight: 37.92 kDa
Atom Count: 2,683
Modeled Residue Count: 325
Deposited Residue Count: 341
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-ribofuranosylaminobenzene 5'-phosphate synthase	A [auth AAA]	341	Streptomyces kaniharaensis	Mutation(s): 1 Gene Names: cof6, F7Q99_03185
UniProt
Find proteins for A0A5S9CYM0 (Streptomyces kaniharaensis) Explore A0A5S9CYM0 Go to UniProtKB: A0A5S9CYM0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5S9CYM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MZU (Subject of Investigation/LOI) Query on MZU Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	4-azanyl-3-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-1~{H}-pyrazole-5-carboxylic acid C₉ H₁₄ N₃ O₉ P KFBPDQGSYVBBLS-UOQNBVRUSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
DPO (Subject of Investigation/LOI) Query on DPO Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain K [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA] E [auth AAA] G [auth AAA] H [auth AAA] K [auth AAA] D [auth AAA], E [auth AAA], G [auth AAA], H [auth AAA], K [auth AAA], M [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], I [auth AAA], J [auth AAA], L [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain F [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain L [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth AAA] MOL2 format, chain N [auth AAA] mmCIF format, chain N [auth AAA]	N [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth AAA] Interactions & Density Focus chain N [auth AAA]