Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

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This is version 1.2 of the entry. See complete history


Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus.

Yao, M.Ose, T.Sugimoto, H.Horiuchi, A.Nakagawa, A.Wakatsuki, S.Yokoi, D.Murakami, T.Honma, M.Tanaka, I.

(2000) J Biol Chem 275: 34557-34565

  • DOI: https://doi.org/10.1074/jbc.M004681200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The pyridoxal 5'-phosphate (PLP)-dependent enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD) catalyzes a reaction that involves a ring opening of cyclopropanoid amino acid, yielding alpha-ketobutyrate and ammonia. Unlike other PLP-dependent enzymes, this enzyme has no alpha-hydrogen atom in the substrate. Thus, a unique mechanism for the bond cleavage is expected. The crystal structure of ACCD from Hansenula saturnus has been determined at 2.0 A resolution by the multiple wavelength anomalous diffraction method using mercury atoms as anomalous scatterers. The model was built on the electron density map, which was obtained by the density averaging of multiple crystal forms. The final model was refined to an R-factor of 22.5% and an R(free)-factor of 26.8%. The ACCD folds into two domains, each of which has an open twisted alpha/beta structure similar to the beta-subunit of tryptophan synthase. However, in ACCD, unlike in other members of the beta family of PLP-dependent enzymes, PLP is buried deep in the molecule. The structure provides the first view of the catalytic center of the cyclopropane ring opening.

  • Organizational Affiliation

    Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
341Cyberlindnera saturnusMutation(s): 0 
Find proteins for Q7M523 (Cyberlindnera saturnus)
Explore Q7M523 
Go to UniProtKB:  Q7M523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M523
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.38α = 90
b = 269.37β = 90
c = 186.62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance