3DHG | pdb_00003dhg

Crystal Structure of Toluene 4-Monoxygenase Hydroxylase

PDB DOI: https://doi.org/10.2210/pdb3DHG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ectopseudomonas mendocina
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-17 Released: 2008-12-30
Deposition Author(s): Bailey, L.J., Mccoy, J.G., Phillips Jr., G.N., Fox, B.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.214 (Depositor), 0.223 (DCC)
R-Value Work:
0.164 (Depositor)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structural consequences of effector protein complex formation in a diiron hydroxylase.

Bailey, L.J., McCoy, J.G., Phillips Jr., G.N., Fox, B.G.

(2008) Proc Natl Acad Sci U S A 105: 19194-19198

PubMed: 19033467 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0807948105
Primary Citation Related Structures:
3DHG, 3DHH, 3DHI

PubMed Abstract:
Carboxylate-bridged diiron hydroxylases are multicomponent enzyme complexes responsible for the catabolism of a wide range of hydrocarbons and as such have drawn attention for their mechanism of action and potential uses in bioremediation and enzymatic synthesis. These enzyme complexes use a small molecular weight effector protein to modulate the function of the hydroxylase. However, the origin of these functional changes is poorly understood. Here, we report the structures of the biologically relevant effector protein-hydroxylase complex of toluene 4-monooxygenase in 2 redox states. The structures reveal a number of coordinated changes that occur up to 25 A from the active site and poise the diiron center for catalysis. The results provide a structural basis for the changes observed in a number of the measurable properties associated with effector protein binding. This description provides insight into the functional role of effector protein binding in all carboxylate-bridged diiron hydroxylases.

Organizational Affiliation

Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544, USA.

Macromolecule Content

Total Structure Weight: 212.95 kDa
Atom Count: 16,033
Modeled Residue Count: 1,754
Deposited Residue Count: 1,822
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
toluene 4-monooxygenase hydroxylase alpha subunit	A, D	500	Ectopseudomonas mendocina	Mutation(s): 0 Gene Names: tmoA EC: 1.14.13.236
UniProt
Find proteins for Q00456 (Ectopseudomonas mendocina) Explore Q00456 Go to UniProtKB: Q00456
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00456
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
toluene 4-monooxygenase hydroxylase beta subunit	B, E	327	Ectopseudomonas mendocina	Mutation(s): 0 Gene Names: tmoE EC: 1.14.13.236
UniProt
Find proteins for Q00460 (Ectopseudomonas mendocina) Explore Q00460 Go to UniProtKB: Q00460
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00460
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
toluene 4-monooxygenase hydroxylase gamma subunit	C, F	84	Ectopseudomonas mendocina	Mutation(s): 0 Gene Names: tmoB EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
Find proteins for Q00457 (Ectopseudomonas mendocina) Explore Q00457 Go to UniProtKB: Q00457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	G [auth A], H [auth A], O [auth D], P [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth D] Focus chain P [auth D]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain N [auth C] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth C], R [auth E], S [auth E], T [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214 (Depositor), 0.223 (DCC)
R-Value Work: 0.164 (Depositor)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.822	α = 90
b = 181.481	β = 107.62
c = 89.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-01-30
Changes: Structure summary
Version 1.3: 2016-12-14
Changes: Structure summary
Version 1.4: 2017-10-25
Changes: Refinement description
Version 1.5: 2024-02-21
Changes: Data collection, Database references, Derived calculations