7DL3 | pdb_00007dl3

The structure of 3,5-DAHDHcca complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of beta-Amino Acids.

Liu, N.Wu, L.Feng, J.Sheng, X.Li, J.Chen, X.Li, J.Liu, W.Zhou, J.Wu, Q.Zhu, D.

(2021) Angew Chem Int Ed Engl 60: 10203-10210

  • DOI: https://doi.org/10.1002/anie.202017225
  • Primary Citation Related Structures: 
    7DL0, 7DL1, 7DL3, 7DL7

  • PubMed Abstract: 

    Amino acid dehydrogenases (AADHs) have shown considerable potential as biocatalysts in the asymmetric synthesis of chiral amino acids. However, compared to the widely studied α-AADHs, limited knowledge is available about β-AADHs that enable the synthesis of β-amino acids. Herein, we report the crystal structures of a l-erythro-3,5-diaminohexanoate dehydrogenase and its variants, the only known member of β-AADH family. Crystal structure analysis, site-directed mutagenesis studies and quantum chemical calculations revealed the differences in the substrate binding and catalytic mechanism from α-AADHs. A number of rationally engineered variants were then obtained with improved activity (by 110-800 times) toward various aliphatic β-amino acids without an enantioselectivity trade-off. Two β-amino acids were prepared by using the outstanding variants with excellent enantioselectivity (>99 % ee) and high isolated yields (86-87 %). These results provide important insights into the molecular mechanism of 3,5-DAHDH, and establish a solid foundation for further design of β-AADHs for the asymmetric synthesis of β-amino acids.


  • Organizational Affiliation
    • National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, and, National Technology Innovation Center for Synthetic Biology, Tianjin, 300308, China.

Macromolecule Content 

  • Total Structure Weight: 158.19 kDa 
  • Atom Count: 11,770 
  • Modeled Residue Count: 1,407 
  • Deposited Residue Count: 1,432 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3,5-diaminohexanoate dehydrogenase
A, B, C, D
358Candidatus Cloacimonas acidaminovorans str. EvryMutation(s): 0 
Gene Names: kddCLOAM1348
EC: 1.4.1.11
UniProt
Find proteins for B0VJ11 (Cloacimonas acidaminovorans (strain Evry))
Explore B0VJ11 
Go to UniProtKB:  B0VJ11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0VJ11
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.594α = 90
b = 122.037β = 94.847
c = 114.645γ = 90
Software Package:
Software NamePurpose
HKL-3000data processing
HKL-3000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2177020792

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description