8XHD

Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor and L-glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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

Structural and mechanistic investigations on CC bond forming alpha-oxoamine synthase allowing L-glutamate as substrate.

Zhang, D.K.Song, K.Y.Yan, Y.Q.Zheng, J.T.Xu, J.Da, L.T.Xu, M.J.

(2024) Int J Biol Macromol 268: 131696-131696

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.131696
  • Primary Citation of Related Structures:  
    8I7U, 8XHA, 8XHD, 8XHK

  • PubMed Abstract: 

    Carbon‑carbon bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase, named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase (AOS) family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to the substrates PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with β-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.


  • Organizational Affiliation

    Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
8-amino-7-oxononanoate synthase
A, B
398Streptomyces albogriseolus 1-36Mutation(s): 1 
Gene Names: alb29
EC: 2.3.1.47
UniProt
Find proteins for A0A6B9KSL0 (Streptomyces albogriseolus)
Explore A0A6B9KSL0 
Go to UniProtKB:  A0A6B9KSL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6B9KSL0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGU (Subject of Investigation/LOI)
Query on PGU

Download Ideal Coordinates CCD File 
C [auth A]N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid
C13 H19 N2 O9 P
JMRKOGDJNHPMHS-JTQLQIEISA-N
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
D [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.734α = 90
b = 117.734β = 90
c = 145.018γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)ChinaNo. 2022YFC2804100

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references