5FDF

Crystal structure of the monoclinic form of Thermotoga maritima Acetyl Esterase TM0077 (apo structure) at 1.76 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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 194: 434-445

  • DOI: 10.1016/j.jsb.2016.04.008
  • Primary Citation of Related Structures:  
    5FDF, 5HFN

  • PubMed Abstract: 
  • The carbohydrate esterase family 7 (CE7) belonging to the α/β hydrolase superfamily contains a structurally conserved loop extension element relative to the canonical α/β hydrolase fold. This element called the β-interface loop contributes 20-30% of the total buried surface area at intersubunit interfaces of the functional hexameric state ...

    The carbohydrate esterase family 7 (CE7) belonging to the α/β hydrolase superfamily contains a structurally conserved loop extension element relative to the canonical α/β hydrolase fold. This element called the β-interface loop contributes 20-30% of the total buried surface area at intersubunit interfaces of the functional hexameric state. To test whether this loop is an enabling region for the structure and function of the oligomeric assembly, we designed a truncation variant of the thermostable CE7 acetyl esterase from Thermotoga maritima (TmAcE). Although deletion of 26 out of 40 residues in the loop had little impact on the hexamer formation, the variant exhibited altered dynamics of the oligomeric assembly and a loss of thermal stability. Furthermore, the mutant lacked catalytic activity. Crystal structures of the variant and a new crystal form of the wild type protein determined at 2.75Å and 1.76Å, respectively, provide a rationale for the properties of the variant. The hexameric assembly in the variant is identical to that of the wild type and differed only in the lack of buried surface area interactions at the original intersubunit interfaces. This is accompanied by disorder in an extended region of the truncated loop that consequently induces disorder in the neighboring oxyanion hole loop. Overall, the results suggest that the β-interface loop in CE7 enzymes is dispensable for the oligomeric assembly. Rather, the loop extension event was evolutionarily selected to regulate activity, conformational flexibility and thermal stability.


    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 maritimaMutation(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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.76α = 90
b = 116.2β = 109.97
c = 103.29γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing
MOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references