2IND | pdb_00002ind

Mn(II) Reconstituted Toluene/o-xylene Monooxygenase Hydroxylase X-ray Crystal Structure

PDB DOI: https://doi.org/10.2210/pdb2IND/pdb

Classification: OXIDOREDUCTASE
Organism(s): Stutzerimonas stutzeri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-10-06 Released: 2006-12-05
Deposition Author(s): McCormick, M.S., Sazinsky, M.H., Condon, K.L., Lippard, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.246 (Depositor)
R-Value Work:
0.217 (Depositor), 0.231 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior.

McCormick, M.S., Sazinsky, M.H., Condon, K.L., Lippard, S.J.

(2006) J Am Chem Soc 128: 15108-15110

PubMed: 17117860 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja064837r
Primary Citation Related Structures:
2INC, 2IND

PubMed Abstract:
We report the X-ray crystal structures of native and manganese(II)-reconstituted toluene/o-xylene monooxygenase hydroxylase (ToMOH) from Pseudomonas stutzeri OX1 to 1.85 and 2.20 A resolution, respectively. The structures reveal that reduction of the dimetallic active site is accompanied by a carboxylate shift and alteration of the coordination environment for dioxygen binding and activation. A rotamer shift in a strategically placed asparagine 202 accompanies dimetallic center reduction and is proposed to influence protein component interactions. This rotamer shift is conserved between ToMOH and the corresponding residue in methane monooxygenase hydroxylase (MMOH). Previously unidentified hydrophobic pockets similar to those present in MMOH are assigned.

Organizational Affiliation

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Macromolecule Content

Total Structure Weight: 104.65 kDa
Atom Count: 7,508
Modeled Residue Count: 897
Deposited Residue Count: 897
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toluene, o-xylene monooxygenase oxygenase subunit	A	491	Stutzerimonas stutzeri	Mutation(s): 0 Gene Names: touA
UniProt
Find proteins for O87798 (Stutzerimonas stutzeri) Explore O87798 Go to UniProtKB: O87798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87798
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toluene, o-xylene monooxygenase oxygenase subunit	B	323	Stutzerimonas stutzeri	Mutation(s): 0 Gene Names: touE
UniProt
Find proteins for O87802 (Stutzerimonas stutzeri) Explore O87802 Go to UniProtKB: O87802
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87802
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TouB protein	C	83	Stutzerimonas stutzeri	Mutation(s): 0 Gene Names: touB
UniProt
Find proteins for O87799 (Stutzerimonas stutzeri) Explore O87799 Go to UniProtKB: O87799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87799
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246 (Depositor)
R-Value Work: 0.217 (Depositor), 0.231 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.521	α = 90
b = 182.521	β = 90
c = 67.792	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-12-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description