Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 

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Structure of Cyanase Reveals that a Novel Dimeric and Decameric Arrangement of Subunits is Required for Formation of the Enzyme Active Site

Walsh, M.A.Otwinowski, Z.Perrakis, A.Anderson, P.M.Joachimiak, A.

(2000) Structure 8: 505

  • DOI: https://doi.org/10.1016/s0969-2126(00)00134-9
  • Primary Citation of Related Structures:  
    1DW9, 1DWK

  • PubMed Abstract: 

    Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

  • Organizational Affiliation

    Biosciences Division/Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
156Escherichia coliMutation(s): 0 
Find proteins for P00816 (Escherichia coli (strain K12))
Explore P00816 
Go to UniProtKB:  P00816
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00816
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
EA [auth G]
FA [auth G]
HA [auth H]
BA [auth F],
CA [auth F],
EA [auth G],
FA [auth G],
HA [auth H],
IA [auth H],
JA [auth H],
L [auth A],
LA [auth I],
M [auth A],
MA [auth I],
O [auth B],
OA [auth J],
P [auth B],
PA [auth J],
QA [auth J],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth E]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
K [auth A]
KA [auth I]
AA [auth F],
DA [auth G],
GA [auth H],
K [auth A],
KA [auth I],
N [auth B],
NA [auth J],
Q [auth C],
S [auth D],
W [auth E]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.34α = 70.3
b = 81.03β = 72.2
c = 82.3γ = 66.4
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-08-21
    Changes: Data collection, Database references