Crystal structure of ACC deaminase complexed with substrate analog b-chloro-D-alanine

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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Structural Analysis of Pseudomonas 1-Aminocyclopropane-1-carboxylate Deaminase Complexes: Insight into the Mechanism of a Unique Pyridoxal-5'-phosphate Dependent Cyclopropane Ring-Opening Reaction

Karthikeyan, S.Zhou, Q.Zhao, Z.Kao, C.L.Tao, Z.Robinson, H.Liu, H.W.Zhang, H.

(2004) Biochemistry 43: 13328-13339

  • DOI: https://doi.org/10.1021/bi048878g
  • Primary Citation of Related Structures:  
    1TYZ, 1TZ2, 1TZJ, 1TZK, 1TZM

  • PubMed Abstract: 

    1-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.

  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-aminocyclopropane-1-carboxylate deaminase
A, B, C, D
338Pseudomonas sp. ACPMutation(s): 0 
Find proteins for Q00740 (Pseudomonas sp. (strain ACP))
Explore Q00740 
Go to UniProtKB:  Q00740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00740
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth C],
N [auth D]
C8 H10 N O6 P
Query on C2N

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
C3 H6 Cl N O2
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B],
M [auth D]
O4 S
Query on NAK

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]
C3 H5 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.64α = 90
b = 68.263β = 90
c = 349.748γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations