5GMX

Crystal structure of a family VIII carboxylesterase

• PDB DOI: https://doi.org/10.2210/pdb5GMX/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-18 Released: 2017-07-26 
• Deposition Author(s): An, Y.J., Cha, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Crystal structure of EstSRT1, a family VIII carboxylesterase displaying hydrolytic activity toward oxyimino cephalosporins

Cha, S.S., An, Y.J.

(2016) Biochem Biophys Res Commun 478: 818-824

• PubMed: 27501751 
• DOI: https://doi.org/10.1016/j.bbrc.2016.08.031
• Primary Citation of Related Structures:  
  5GMX


• PubMed Abstract: 
  

  EstSRT1 is a family VIII carboxylesterase that hydrolyzes oxyimino third- and fourth-generation cephalosporins, first-generation cephalosporins and ester substrates. According to the crystal structure of EstSRT1 (2.0-Å resolution), this protein contains a large α/β domain and a small α-helical domain and harbors three catalytic residues (Ser71, Lys74, and Tyr160) in the cavity at the domain interface, similarly to other family VIII carboxylesterases. Comparison of the structures of EstSRT1 and EstU1, a family VIII carboxylesterase with no hydrolytic activity toward bulky oxyimino cephalosporins, revealed that EstSRT1 has a smaller active site, despite its extended substrate range. The B-factors of the active site segments that could potentially contact with the oxyimino groups and the R2 side chains of oxyimino cephalosporins are higher in EstSRT1 than in EstU1, thus suggesting the role of the active site's structural flexibility in the extension of EstSRT1's substrate spectrum.

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Organizational Affiliation: 

Department of Chemistry & Nano Science, Ewha Womans University, Seoul, 03760, Republic of Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.16 kDa 
• Atom Count: 5,871 
• Modelled Residue Count: 738 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase	A, B	398	uncultured bacterium	Mutation(s): 0  EC: 3.1.1.1
UniProt
Find proteins for A0A0G2RKR9 (uncultured bacterium) Explore A0A0G2RKR9  Go to UniProtKB:  A0A0G2RKR9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMS	C [auth A], D [auth B]	phenylmethanesulfonic acid C7 H8 O3 S NIXKBAZVOQAHGC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.128	α = 90
b = 95.149	β = 90
c = 99.943	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-26 
Deposition Author(s): An, Y.J., Cha, S.S.

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references