5JIB

Crystal structure of the Thermotoga maritima acetyl esterase (TM0077) complex with a substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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Literature

Crystal structure of Thermotoga maritima acetyl esterase complex with a substrate analog: Insights into the distinctive substrate specificity in the CE7 carbohydrate esterase family

Singh, M.K.Manoj, N.

(2016) Biochem Biophys Res Commun 476: 63-68

  • DOI: 10.1016/j.bbrc.2016.05.061
  • Primary Citation of Related Structures:  
    5JIB

  • PubMed Abstract: 
  • The carbohydrate esterase family 7 (CE7) members are acetyl esterases that possess unusual substrate specificity for cephalosporin C and 7-amino-cephalosporanic acid. This family containing the α/β hydrolase fold has a distinctive substrate profile that allows it to carry out hydrolysis of esters containing diverse alcohol moieties while maintaining narrow specificity for an acetate ester ...

    The carbohydrate esterase family 7 (CE7) members are acetyl esterases that possess unusual substrate specificity for cephalosporin C and 7-amino-cephalosporanic acid. This family containing the α/β hydrolase fold has a distinctive substrate profile that allows it to carry out hydrolysis of esters containing diverse alcohol moieties while maintaining narrow specificity for an acetate ester. Here we investigate the structural basis of this preference for small acyl groups using the crystal structure of the thermostable Thermotoga maritima CE7 acetyl esterase (TmAcE) complexed with a non-cognate substrate analog. The structure determined at 1.86 Å resolution provides direct evidence for the location of the largely hydrophobic and rigid substrate binding pocket in this family. Furthermore, a three-helix insertion domain near the catalytic machinery shapes the substrate binding site. The structure reveals two residues (Pro228 and Ile276) which constitute a hydrophobic rigid binding surface for the acyl group of the ester and thus restricts the size of the acyl group that be accommodated. In combination with previous literature on kinetic properties of the enzyme, our studies suggest that these residues determine the unique specificity of the TmAcE for short straight chain esters. The structure provides a template for focused attempts to engineer the CE7 enzymes for enhanced stability, selectivity or activity for biocatalytic applications.


    Related Citations: 
    • An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability.
      Singh, M.K., Manoj, N.
      (2016) J Struct Biol --: --

    Organizational Affiliation

    Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India. Electronic address: nmanoj@iitm.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cephalosporin-C deacetylase
A, B, C, D, E, F
A, B, C, D, E, F
337Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: axeATM_0077
EC: 3.1.1.41 (PDB Primary Data), 3.1.1.72 (PDB Primary Data)
UniProt
Find proteins for Q9WXT2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXT2 
Go to UniProtKB:  Q9WXT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WXT2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OIA
Query on OIA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
L [auth F]
[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid
C10 H9 N O3
ILGMGHZPXRDCCS-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.81α = 90
b = 115.78β = 109.98
c = 103.2γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2017-03-01 
  • Deposition Author(s): Manoj, N.

Funding OrganizationLocationGrant Number
Department of Biotechnology, Govt. of IndiaIndiaBT/PR13805/PID/06/550/2010

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release