5Z75 | pdb_00005z75

Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.

PDB DOI: https://doi.org/10.2210/pdb5Z75/pdb

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

Deposited: 2018-01-27 Released: 2018-08-22
Deposition Author(s): Nakano, S., Motoyama, T., Miyashita, Y., Ishizuka, Y., Matsuo, N., Tokiwa, H., Shinoda, S., Asano, Y., Ito, S.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.242 (DCC)
R-Value Work:
0.193 (Depositor), 0.199 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.

Nakano, S., Motoyama, T., Miyashita, Y., Ishizuka, Y., Matsuo, N., Tokiwa, H., Shinoda, S., Asano, Y., Ito, S.

(2018) Biochemistry 57: 3722-3732

PubMed: 29787243 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.8b00339
Primary Citation Related Structures:
5Z75, 5Z76

PubMed Abstract:
The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full-consensus design (FCD) and ancestral-sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial l-threonine 3-dehydrogenases (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1, and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD ⁺ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH); the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5 °C higher than that of CnTDH, respectively, and the dissociation constants toward NAD ⁺ of FcTDH-N1 and AncTDH were 2- and 7-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.

Organizational Affiliation

Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.

Macromolecule Content

Total Structure Weight: 151.94 kDa
Atom Count: 10,523
Modeled Residue Count: 1,224
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Artificial L-threonine 3-dehydrogenase	A, B, C, D	327	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D]	E [auth A], H [auth B], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth D]
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	I [auth B], L [auth C], O [auth D]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] G [auth A] J [auth B] K [auth B] M [auth C] F [auth A], G [auth A], J [auth B], K [auth B], M [auth C], P [auth D], Q [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]