1XVB

soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Product Bound Structures of the Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath): Protein Motion in the Alpha-Subunit

Sazinsky, M.H.Lippard, S.J.

(2005) J.Am.Chem.Soc. 127: 5814-5825

  • DOI: 10.1021/ja044099b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities ...

    The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.


    Organizational Affiliation

    Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase component A alpha chain
A, B
527Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: mmoX
EC: 1.14.13.25
Find proteins for P22869 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P22869
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase component A beta chain
C, D
389Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: mmoY
EC: 1.14.13.25
Find proteins for P18798 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P18798
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase component A gamma chain
E, F
170Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: mmoZ
EC: 1.14.13.25
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P11987
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BR
Query on 3BR

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C
1-BROMOPROPANE
C3 H7 Br
CYNYIHKIEHGYOZ-UHFFFAOYSA-N
 Ligand Interaction
BHL
Query on BHL

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Download CCD File 
A, B
6-BROMOHEXAN-1-OL
6-BROMOHEXANOL
C6 H13 Br O
FCMCSZXRVWDVAW-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BBX
Query on BBX

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B
1-BROMOETHANE
C2 H5 Br
RDHPKYGYEGBMSE-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
BBU
Query on BBU

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A
1-BROMOBUTANE
C4 H9 Br
MPPPKRYCTPRNTB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.632α = 90.00
b = 171.867β = 90.00
c = 220.622γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance