8AQ0 | pdb_00008aq0

Crystal structure of L-N-Carbamoylase from Sinorhizobium meliloti mutant L217G/F329C

PDB DOI: https://doi.org/10.2210/pdb8AQ0/pdb

Classification: HYDROLASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-08-11 Released: 2022-11-16
Deposition Author(s): Rozeboom, H.J., Mayer, C.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.238 (Depositor), 0.241 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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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

Selecting Better Biocatalysts by Complementing Recoded Bacteria.

Rubini, R., Jansen, S.C., Beekhuis, H., Rozeboom, H.J., Mayer, C.

(2023) Angew Chem Int Ed Engl 62: e202213942-e202213942

PubMed: 36342942 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202213942
Primary Citation Related Structures:
8APZ, 8AQ0

PubMed Abstract:
In vivo selections are powerful tools for the directed evolution of enzymes. However, the need to link enzymatic activity to cellular survival makes selections for enzymes that do not fulfill a metabolic function challenging. Here, we present an in vivo selection strategy that leverages recoded organisms addicted to non-canonical amino acids (ncAAs) to evolve biocatalysts that can provide these building blocks from synthetic precursors. We exemplify our platform by engineering carbamoylases that display catalytic efficiencies more than five orders of magnitude higher than those observed for the wild-type enzyme for ncAA-precursors. As growth rates of bacteria under selective conditions correlate with enzymatic activities, we were able to elicit improved variants from populations by performing serial passaging. By requiring minimal human intervention and no specialized equipment, we surmise that our strategy will become a versatile tool for the in vivo directed evolution of diverse biocatalysts.

Organizational Affiliation

Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 94.85 kDa
Atom Count: 6,354
Modeled Residue Count: 820
Deposited Residue Count: 874
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-carbamoyl-L-amino-acid hydrolase	A, B	437	Sinorhizobium meliloti	Mutation(s): 2 Gene Names: hyuC EC: 3.5.1.87
UniProt
Find proteins for Q6DTN4 (Rhizobium meliloti) Explore Q6DTN4 Go to UniProtKB: Q6DTN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DTN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NV6 Query on NV6 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	(2~{S})-2-(aminocarbonylamino)-3-(4-hydroxyphenyl)propanoic acid C₁₀ H₁₂ N₂ O₄ PNLKYZVGQWCHBH-QMMMGPOBSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], H [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], I [auth B], K [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]