3Q14

Toluene 4 monooxygenase HD Complex with p-cresol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic analysis of active site contributions to regiospecificity in the diiron enzyme toluene 4-monooxygenase.

Bailey, L.J.Acheson, J.F.McCoy, J.G.Elsen, N.L.Phillips, G.N.Fox, B.G.

(2012) Biochemistry 51: 1101-1113

  • DOI: 10.1021/bi2018333
  • Primary Citation of Related Structures:  
    3Q14, 3Q2A, 3Q3M, 3Q3N, 3Q3O, 3RI7, 3RMK

  • PubMed Abstract: 
  • Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric μ-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201 ...

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric μ-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH(2)-benzoate and p-Br-benzoate showed a μ-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a π-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 Å) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential contribution to product release.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENTAETHYLENE GLYCOLA500Pseudomonas mendocinaMutation(s): 0 
Gene Names: Q00456tmoA
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein EB307Pseudomonas mendocinaMutation(s): 0 
Gene Names: Q00460tmoE
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein BC84Pseudomonas mendocinaMutation(s): 0 
Gene Names: Q00457tmoB
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein DD [auth E]103Pseudomonas mendocinaMutation(s): 0 
Gene Names: Q00459tmoD
EC: 1.14.13
UniProt
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Go to UniProtKB:  Q00459
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCR
Query on PCR

Download Ideal Coordinates CCD File 
G [auth A], H [auth E]P-CRESOL
C7 H8 O
IWDCLRJOBJJRNH-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.363α = 90
b = 116.023β = 90
c = 180.711γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2012-02-29
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description