1IAY | pdb_00001iay

CRYSTAL STRUCTURE OF ACC SYNTHASE COMPLEXED WITH COFACTOR PLP AND INHIBITOR AVG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.290 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5'-phosphate provide new insight into catalytic mechanisms

Huai, Q.Xia, Y.Chen, Y.Callahan, B.Li, N.Ke, H.

(2001) J Biological Chem 276: 38210-38216

  • DOI: https://doi.org/10.1074/jbc.M103840200
  • Primary Citation Related Structures: 
    1IAX, 1IAY

  • PubMed Abstract: 

    The structures of tomato 1-aminocyclopropane-1-carboxylate synthase (ACS) in complex with either cofactor pyridoxal-5'-phosphate (PLP) or both PLP and inhibitor aminoethoxyvinylglycine have been determined by x-ray crystallography. The structures showed good conservation of the catalytic residues, suggesting a similar catalytic mechanism for ACS and other PLP-dependent enzymes. However, the proximity of Tyr152 to the C-gamma-S bond of model substrate S-adenosylmethionine implies its critical role in the catalysis. The concerted accomplishment of catalysis by cofactor PLP and a protein residue, as proposed on the basis of the ACS structures in this paper, may represent a general scheme for the diversity of PLP-dependent catalyses. PLP-dependent enzymes have been categorized into four types of folds. A structural comparison revealed that a core fragment of ACS in fold type I is superimposable over tryptophan synthase beta subunit in fold type II and mouse ornithine decarboxylase in fold type III, thus suggesting a divergent evolution of PLP-dependent enzymes.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599-7260, USA.

Macromolecule Content 

  • Total Structure Weight: 48.7 kDa 
  • Atom Count: 3,394 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 428 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2428Solanum lycopersicumMutation(s): 0 
EC: 4.4.1.14
UniProt
Find proteins for P18485 (Solanum lycopersicum)
Explore P18485 
Go to UniProtKB:  P18485
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18485
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP



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

Query on AVG



Download:Ideal Coordinates CCD File
C [auth A]2-AMINO-4-(2-AMINO-ETHOXY)-BUTYRIC ACID
C6 H14 N2 O3
FDDYPVBIHWFLOI-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.290 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.1α = 90
b = 123.1β = 90
c = 106.8γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary