9AZA | pdb_00009aza

Crystal structure of LolTv4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Enzymatic Synthesis of Unprotected alpha , beta-Diamino Acids via Direct Asymmetric Mannich Reactions.

Liu, S.Gao, J.Zou, Y.Hai, Y.

(2024) J Am Chem Soc 146: 20263-20269

  • DOI: https://doi.org/10.1021/jacs.4c05581
  • Primary Citation Related Structures: 
    9AZA, 9AZB

  • PubMed Abstract: 

    α,β-Diamino acids are important structural motifs and building blocks for numerous bioactive natural products, peptidomimetics, and pharmaceuticals, yet efficient asymmetric synthesis to access these stereoarrays remains a challenge. Herein, we report the development of a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is engineered to catalyze stereoselective Mannich-type reactions between free α-amino acids and enolizable cyclic imines. This biocatalyst enabled one-step asymmetric enzymatic synthesis of the unusual pyrrolidine-containing amino acid L-tambroline at gram-scale with high enantio- and diastereocontrol. Furthermore, this enzymatic platform is capable of utilizing a diverse range of α-amino acids as the Mannich donor and various cyclic imines as the acceptor. By coupling with different imine-generating enzymes, we established versatile biocatalytic cascades and demonstrated a general, concise, versatile, and atom-economic approach to access unprotected α,β-diamino acids, including structurally complex α,α-disubstituted α,β-diamino acids with contiguous stereocenters.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.

Macromolecule Content 

  • Total Structure Weight: 53.19 kDa 
  • Atom Count: 3,142 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 474 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aminotransferase, class V/Cysteine desulfurase474Penicillium expansumMutation(s): 0 
Gene Names: PEX2_110450
UniProt
Find proteins for A0A0A2J6G6 (Penicillium expansum)
Explore A0A0A2J6G6 
Go to UniProtKB:  A0A0A2J6G6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A2J6G6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
(Subject of Investigation/LOI)

Query on PLP



Download:Ideal Coordinates CCD File
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.239α = 90
b = 74.239β = 90
c = 154.669γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM151205

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references