Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 232 kDa 
• Atom Count: 16,113 
• Modelled Residue Count: 1,942 
• Deposited Residue Count: 2,022 
• Unique protein chains: 1

 5GMA

Crystal structure of the P228A variant of Thermotoga maritima acetyl esterase

• PDB DOI:  https://doi.org/10.2210/pdb5GMA/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-13 Released: 2017-06-21 
• Deposition Author(s): Manoj, N.
• Funding Organization(s): Department of Biotechnology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.214 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Structural role of a conserved active site cis proline in the Thermotoga maritima acetyl esterase from the carbohydrate esterase family 7

Singh, M.K., Manoj, N.

(2017) Proteins 85: 694-708

• PubMed: 28097692 
• DOI: https://doi.org/10.1002/prot.25249
• Primary Citation of Related Structures:  
  5GMA


• PubMed Abstract: 
  

A conserved cis proline residue located in the active site of Thermotoga maritima acetyl esterase (TmAcE) from the carbohydrate esterase family 7 (CE7) has been substituted by alanine. The residue was known to play a crucial role in determining the catalytic properties of the enzyme. To elucidate the structural role of the residue, the crystal structure of the Pro228Ala variant (TmAcE _P228A ) was determined at 2.1 Å resolution. The replacement does not affect the overall secondary, tertiary, and quaternary structures and moderately decreases the thermal stability. However, the wild type cis conformation of the 227-228 peptide bond adopts a trans conformation in the variant. Other conformational changes in the tertiary structure are restricted to residues 222-226, preceding this peptide bond and are located away from the active site. Overall, the results suggest that the conserved proline residue is responsible for the cis conformation of the peptide and shapes the geometry of the active site. Elimination of the pyrrolidine ring results in the loss of van der Waals and hydrophobic interactions with both the alcohol and acyl moeities of the ester substrate, leading to significant impairment of the activity and perturbation of substrate specificity. Furthermore, a cis-to-trans conformational change arising out of residue changes at this position may be associated with the evolution of divergent activity, specificity, and stability properties of members constituting the CE7 family. Proteins 2017; 85:694-708. © 2016 Wiley Periodicals, Inc.

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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 194: 434

• 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

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Organizational Affiliation: 

Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cephalosporin-C deacetylase	A, B, C, D, E, F	337	Thermotoga maritima MSB8	Mutation(s): 1  Gene Names: axeA, TM_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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	G [auth C], H [auth D], I [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.214 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.76	α = 90
b = 115.69	β = 110.21
c = 103.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Manoj, N.

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Funding Organization	Location	Grant Number
Department of Biotechnology	India	BT/PR13805/PID/06/550/2010

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release