3P9U | pdb_00003p9u

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.282 (Depositor), 0.281 (DCC)
R-Value Work:
0.238 (Depositor), 0.237 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.23052
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93L51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.281 (DCC)
R-Value Work: 0.238 (Depositor), 0.237 (DCC)
R-Value Observed: 0.240 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Revision History (Full details and data files)

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