4YJI

The Crystal Structure of a Bacterial Aryl Acylamidase Belonging to the Amidase signature (AS) enzymes family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure analysis of a bacterial aryl acylamidase belonging to the amidase signature enzyme family

Lee, S.Park, E.-H.Ko, H.-J.Bang, W.-G.Kim, H.Y.Kim, K.H.Choi, I.-G.

(2015) Biochem.Biophys.Res.Commun. 467: 268-274

  • DOI: 10.1016/j.bbrc.2015.09.177
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in comple ...

    The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in complex with the analgesic acetanilide, p-acetaminophenol, at 1.70 Å and 1.73 Å resolutions, respectively. The overall structural fold of AAA was identified as an α/β fold class, exhibiting an open twisted β-sheet core surrounded by α-helices. The asymmetric unit contains one AAA molecule and the monomeric form is functionally active. The core structure enclosing the signature sequence region, including the canonical Ser-cisSer-Lys catalytic triad, is conserved in all members of the Amidase Signature enzyme family. The structure of AAA in a complex with its ligand reveals a unique organization in the substrate-binding pocket. The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence. We identified two residues (Tyr(136) and Thr(330)) that interact with the ligand via water molecules, and a hydrogen-bonding network that explains the catalytic affinity over various aryl acyl compounds. The optimum activity of AAA at pH > 10 suggests that the reaction mechanism employs Lys(84) as the catalytic base to polarize the Ser(187) nucleophile in the catalytic triad.


    Organizational Affiliation

    Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-Dong, Seoungbuk-Gu, Seoul, 136-713, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aryl acylamidase
A
495bacterium CSBL00001Mutation(s): 1 
EC: 3.5.1.13
Find proteins for C3UWD1 (bacterium CSBL00001)
Go to UniProtKB:  C3UWD1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download SDF File 
Download CCD File 
A
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
TYL
Query on TYL

Download SDF File 
Download CCD File 
A
N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL)
C8 H9 N O2
RZVAJINKPMORJF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.167 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.980α = 90.00
b = 75.980β = 90.00
c = 214.710γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata scaling
PHENIXphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release