7QEE | pdb_00007qee

SN243 mutant D415N bound to para-nitrophenyl-Beta-D-glucuronide

PDB DOI: https://doi.org/10.2210/pdb7QEE/pdb

Classification: HYDROLASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-12-02 Released: 2022-11-16
Deposition Author(s): Neun, S., Brear, P., Campbell, E., Omari, K., Wagner, O., Hyvonen, M., Hollfelder, F.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.217 (Depositor), 0.228 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Functional metagenomic screening identifies an unexpected beta-glucuronidase.

Neun, S., Brear, P., Campbell, E., Tryfona, T., El Omari, K., Wagner, A., Dupree, P., Hyvonen, M., Hollfelder, F.

(2022) Nat Chem Biol 18: 1096-1103

PubMed: 35799064 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-022-01071-x
Primary Citation Related Structures:
7QE1, 7QE2, 7QEA, 7QEE, 7QEF, 7QG4

PubMed Abstract:
The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently 'unpredictable' by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >10 ⁷ library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.

Organizational Affiliation

Department of Biochemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 166.62 kDa
Atom Count: 11,451
Modeled Residue Count: 1,476
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SN243	A, B	759	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C3G (Subject of Investigation/LOI) Query on C3G Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	4-nitrophenyl beta-D-glucopyranosiduronic acid C₁₂ H₁₃ N O₉ QSUILVWOWLUOEU-GOVZDWNOSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
BDP (Subject of Investigation/LOI) Query on BDP Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain JA [auth B]	JA [auth B]	beta-D-glucopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-QIUUJYRFSA-N		Interactions Focus chain JA [auth B] Interactions & Density Focus chain JA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] O [auth A] P [auth A] Q [auth A] HA [auth B], IA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain GA [auth B] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]