3Q2A

Toluene 4 monooxygenase HD complex with inhibitor p-aminobenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 

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:  

  • 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 diiro ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein A
A
500Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoA
EC: 1.14.13.236
Find proteins for Q00456 (Pseudomonas mendocina)
Go to UniProtKB:  Q00456
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein E
B
307Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoE
EC: 1.14.13.236
Find proteins for Q00460 (Pseudomonas mendocina)
Go to UniProtKB:  Q00460
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein B
C
84Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoB
EC: 1.14.13.236
Find proteins for Q00457 (Pseudomonas mendocina)
Go to UniProtKB:  Q00457
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein D
E
103Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoD
Find proteins for Q00459 (Pseudomonas mendocina)
Go to UniProtKB:  Q00459
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAB
Query on PAB

Download SDF File 
Download CCD File 
A
4-AMINOBENZOIC ACID
C7 H7 N O2
ALYNCZNDIQEVRV-UHFFFAOYSA-N
 Ligand Interaction
ETE
Query on ETE

Download SDF File 
Download CCD File 
B
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PABKi: ~5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.973α = 90.00
b = 115.437β = 90.00
c = 180.997γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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