8K6H

Crystal structure of e.coli cyanase complex with cyanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Literature

Structural mechanism of Escherichia coli cyanase.

Kim, J.Kim, Y.Park, J.Nam, K.H.Cho, Y.

(2023) Acta Crystallogr D Struct Biol 79: 1094-1108

  • DOI: https://doi.org/10.1107/S2059798323009609
  • Primary Citation of Related Structures:  
    8K6G, 8K6H, 8K6S, 8K6U, 8K6X

  • PubMed Abstract: 

    Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5-1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. In the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.


  • Organizational Affiliation

    Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyanate hydratase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
160Escherichia coli K-12Mutation(s): 0 
Gene Names: cynScntb0340JW0331
EC: 4.2.1.104
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
HA [auth G],
IA [auth G],
JA [auth G],
K [auth A],
KA [auth H],
LA [auth H],
M [auth A],
N [auth A],
NA [auth I],
O [auth A],
PA [auth I],
Q [auth B],
R [auth B],
RA [auth J],
SA [auth J],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
0NM (Subject of Investigation/LOI)
Query on 0NM

Download Ideal Coordinates CCD File 
DA [auth F]
GA [auth G]
L [auth A]
MA [auth H]
OA [auth I]
DA [auth F],
GA [auth G],
L [auth A],
MA [auth H],
OA [auth I],
P [auth B],
QA [auth J],
S [auth C],
V [auth D],
Z [auth E]
cyanic acid
C H N O
XLJMAIOERFSOGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.136α = 70.51
b = 81.066β = 76.37
c = 81.065γ = 65.26
Software Package:
Software NamePurpose
PHENIXrefinement
MxDCdata collection
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A2C301335711

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release