3P9U

Crystal structure of TetX2 from Bacteroides thetaiotaomicron with substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb3P9U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-18 Released: 2011-04-27 
• Deposition Author(s): Walkiewicz, K., Davlieva, M., Sun, C., Lau, K., Shamoo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Crystal structure of Bacteroides thetaiotaomicron TetX2: a tetracycline degrading monooxygenase at 2.8 A resolution.

Walkiewicz, K., Davlieva, M., Wu, G., Shamoo, Y.

(2011) Proteins 79: 2335-2340

• PubMed: 21590745 
• DOI: https://doi.org/10.1002/prot.23052
• Primary Citation of Related Structures:  
  3P9U


• PubMed Abstract: 
  

  We have determined the structure of Bacteroides thetaiotaomicron TetX2 at 2.8 Å resolution, and shown that it is a class A flavin dependent oxidoreductase. TetX2 has broad activity against a range of tetracyclines including one of the most recent tetracyclines, tigecycline (Tygacil ^® ). Comparison of TetX2 with that of the weakly homologous Pseudomonas fluorescens para-hydroxybenzoate hydroxylase (PHBH) (21% identity) shows substantial differences among residues at the substrate binding site although FAD is positioned in a similar conformation between the two enzymes and is poised to carry out catalysis.

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology, Rice University, 6100 Main St. MS-140, Houston, Texas, USA.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 175.72 kDa 
• Atom Count: 11,909 
• Modelled Residue Count: 1,466 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetX2 protein	A, B, C, D	378	Bacteroides thetaiotaomicron	Mutation(s): 2  Gene Names: tetX2 EC: 1.14.13.231
UniProt
Find proteins for Q93L51 (Bacteroides thetaiotaomicron) Explore Q93L51  Go to UniProtKB:  Q93L51

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.7	α = 90
b = 67.33	β = 100.31
c = 153.79	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Walkiewicz, K., Davlieva, M., Sun, C., Lau, K., Shamoo, Y.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary