8I99 | pdb_00008i99

N-carbamoyl-D-amino-acid hydrolase mutant - M4Th3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 
    0.278 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8I99

This is version 1.1 of the entry. See complete history

Literature

Engineering the Thermostability of a d-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of d-Tryptophan.

Hu, J.Chen, X.Zhang, L.Zhou, J.Xu, G.Ni, Y.

(2023) J Agric Food Chem 71: 660-670

  • DOI: https://doi.org/10.1021/acs.jafc.2c07781
  • Primary Citation Related Structures: 
    8I99

  • PubMed Abstract: 

    Employing ancestral sequence reconstruction and consensus sequence analysis, the thermostability of a novel d-carbamoylase derived from Nitratireductor indicus ( Ni HyuC) was engineered through greedy-oriented iterative combinatorial mutagenesis. A mutant S202P/E208D/R277L (M4Th3) was obtained with significantly elevated thermostability. M4Th3 has a half-life of 36.5 h at 40 °C, about 28.5 times of 1.3 h of its parent M4. For the reaction at 40 °C, M4Th3 can catalyze 10 mM N -carbamoyl-d-tryptophan to produce d-tryptophan with a conversion ratio of 96.4% after 12 h, which is significantly higher than 64.1% of M4. MD simulation reveals that new hydrogen bonds emerging from E208D on the surface can increase the hydrophobicity of the protein, leading to improved stability. More importantly, R277L could contribute to enhanced interface stability of homodimeric M4. This study provides a thermostable d-carbamoylase for the "hydantoinase process", which has potential in the industrial synthesis of optically pure natural and non-natural amino acids.


  • Organizational Affiliation
    • Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China.

Macromolecule Content 

  • Total Structure Weight: 138.35 kDa 
  • Atom Count: 9,680 
  • Modeled Residue Count: 1,222 
  • Deposited Residue Count: 1,228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-carbamoyl-D-amino-acid hydrolase
A, B, C, D
307Nitratireductor indicus C115Mutation(s): 3 
Gene Names: NA8A_19058
UniProt
Find proteins for K2NMS4 (Nitratireductor indicus C115)
Explore K2NMS4 
Go to UniProtKB:  K2NMS4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK2NMS4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free:  0.278 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.143α = 84.08
b = 73.548β = 88.2
c = 77.711γ = 89.73
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22077054

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection