7CYS | pdb_00007cys

Crystal structure of barley agmatine coumaroyltransferase (HvACT), an N-acyltransferase in BAHD superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.203 (Depositor) 
  • R-Value Work: 
    0.191 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of barley agmatine coumaroyltransferase, an N-acyltransferase from the BAHD superfamily.

Yamane, M.Takenoya, M.Yajima, S.Sue, M.

(2020) Acta Crystallogr F Struct Biol Commun 76: 590-596

  • DOI: https://doi.org/10.1107/S2053230X20014880
  • Primary Citation Related Structures: 
    7CYS

  • PubMed Abstract: 

    The enzymes of the BAHD superfamily, a large group of acyl-CoA-dependent acyltransferases in plants, are involved in the biosynthesis of diverse secondary metabolites. While the structures of several O-acyltransferases from the BAHD superfamily, such as hydroxycinnamoyl-CoA shikimate hydroxycinnamoyl transferase, have been elucidated, no structural information on N-acyltransferases is available. Hordeum vulgare agmatine coumaroyltransferase (HvACT) is an N-acyltransferase from the BAHD superfamily and is one of the most important enzymes in the secondary metabolism of barley. Here, an apo-form structure of HvACT is reported as the first structure of an N-acyltransferase from the BAHD superfamily. HvACT crystals diffracted to 1.8 Å resolution and belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 57.6, b = 59.5, c = 73.6 Å, α = 90, β = 91.3 , γ = 90°. Like other known BAHD superfamily structures, HvACT contains two domains that adopt a two-layer αβ-sandwich architecture and a solvent-exposed channel that penetrates the enzyme core.


  • Organizational Affiliation
    • Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 51.63 kDa 
  • Atom Count: 3,538 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Agmatine coumaroyltransferase-1470Hordeum vulgareMutation(s): 0 
Gene Names: ACT-1ACT
EC: 2.3.1.64
UniProt
Find proteins for A9ZPJ6 (Hordeum vulgare)
Explore A9ZPJ6 
Go to UniProtKB:  A9ZPJ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9ZPJ6
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.203 (Depositor) 
  • R-Value Work:  0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.632α = 90
b = 59.521β = 91.285
c = 73.627γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary