9IHS | pdb_00009ihs

Microbial transglutaminase mutant - D3C/G283C

PDB DOI: https://doi.org/10.2210/pdb9IHS/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces mobaraensis
Expression System: Corynebacterium glutamicum
Mutation(s): Yes

Deposited: 2024-06-18 Released: 2024-09-18
Deposition Author(s): Suzuki, M., Date, M., Kashiwagi, T., Takahashi, K., Nakamura, A., Tanokura, M., Suzuki, E., Yokoyama, K.
Funding Organization(s): Ajinomoto Co., Inc., Development of Systems and Technology for Advanced Measurement and Analysis (Program-S)-Fund of the Japan Science and Technology Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor), 0.235 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Random mutagenesis and disulfide bond formation improved thermostability in microbial transglutaminase.

Suzuki, M., Date, M., Kashiwagi, T., Takahashi, K., Nakamura, A., Tanokura, M., Suzuki, E., Yokoyama, K.

(2024) Appl Microbiol Biotechnol 108: 478-478

PubMed: 39354113 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s00253-024-13304-1
Primary Citation of Related Structures:
9IHS

PubMed Abstract:
Microbial transglutaminase (MTG) from Streptomyces mobaraensis is widely used in the food and pharmaceutical industries for cross-linking and post-translational modification of proteins. It is believed that its industrial applications could be further broadened by improving its thermostability. In our previous study, we showed that the introduction of structure-based disulfide bonds improved the thermostability of MTG, and we succeeded in obtaining a thermostable mutant, D3C/G283C, with a T ₅₀ (incubation temperature at which 50% of the initial activity remains) 9 °C higher than that of wild-type MTG. In this study, we performed random mutations using D3C/G283C as a template and found several amino acid substitutions that contributed to the improvement of thermostability, and investigated a thermostable mutant (D3C/S101P/G157S/G250R/G283C) with three amino acid mutations in addition to the disulfide bond. The T ₅₀ of this mutant was 10 °C higher than that of the wild type, the optimal temperature for enzymatic reaction was increased to 65 °C compared to 50 °C for the wild type, and the catalytic efficiency (k _cat/K _m) at 37.0 °C was increased from 3.3 × 10 ² M ^-1 s ^-1 for the wild type to 5.9 × 10 ² M ^-1 s ^-1. X-ray crystallography of the D3C/G283C MTG showed no major structural differences against wild-type MTG. Structural differences were found that may contribute to thermostabilization and improve catalytic efficiency. KEY POINTS: • Improved heat resistance is essential to broaden the application of MTG. • The MTG mutant D3C/S101P/G157S/G250R/G283C showed improved thermostability. • X-ray crystallography of the disulfide bridge mutant D3C/G283C MTG was elucidated.

Organizational Affiliation

Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-Shi, Kanagawa, 210-8681, Japan.

Macromolecule Content

Total Structure Weight: 152.84 kDa
Atom Count: 11,885
Modeled Residue Count: 1,324
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-glutamine gamma-glutamyltransferase	A, B, C, D	331	Streptomyces mobaraensis	Mutation(s): 2 EC: 2.3.2.13
UniProt
Find proteins for P81453 (Streptomyces mobaraensis) Explore P81453 Go to UniProtKB: P81453
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81453
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.234 (Depositor), 0.235 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.76	α = 90
b = 117.36	β = 113.028
c = 85.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Ajinomoto Co., Inc.	Japan	--
Development of Systems and Technology for Advanced Measurement and Analysis (Program-S)-Fund of the Japan Science and Technology Agency	Japan	--