7YPM | pdb_00007ypm

Crystal structure of transaminase CC1012 complexed with PLP and L-alanine

PDB DOI: https://doi.org/10.2210/pdb7YPM/pdb

Classification: TRANSFERASE
Organism(s): Caulobacter sp. D5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-08-03 Released: 2023-05-24
Deposition Author(s): Yang, L., Wang, H., Wei, D.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.237 (Depositor), 0.235 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism-Guided Computational Design of omega-Transaminase by Reprograming of High-Energy-Barrier Steps.

Yang, L., Zhang, K., Xu, M., Xie, Y., Meng, X., Wang, H., Wei, D.

(2022) Angew Chem Int Ed Engl 61: e202212555-e202212555

PubMed: 36300723 Search on PubMed
DOI: https://doi.org/10.1002/anie.202212555
Primary Citation Related Structures:
7YPM, 7YPN

PubMed Abstract:
ω-Transaminases (ω-TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism-guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high-energy-barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate-limiting transition state with the aid of the Rosetta design. The 14 top-ranked variants showed 16.9-143-fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660-fold increase in k _cat /K _m and a 1.5-26.8-fold increase in turnover number (TON) towards various indanone derivatives.

Organizational Affiliation

State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China.

Macromolecule Content

Total Structure Weight: 209.46 kDa
Atom Count: 15,347
Modeled Residue Count: 1,816
Deposited Residue Count: 1,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase family protein	A, B, C, D	474	Caulobacter sp. D5	Mutation(s): 5 Gene Names: DMC18_08975
UniProt
Find proteins for A0ACD6BA79 (Caulobacter sp. D5) Explore A0ACD6BA79 Go to UniProtKB: A0ACD6BA79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BA79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	F [auth A] I [auth B] J [auth B] M [auth C] O [auth D] F [auth A], I [auth B], J [auth B], M [auth C], O [auth D], P [auth D]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]