4GAM

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.902 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Control of substrate access to the active site in methane monooxygenase.

Lee, S.J.McCormick, M.S.Lippard, S.J.Cho, U.S.

(2013) Nature 494: 380-384

  • DOI: 10.1038/nature11880

  • PubMed Abstract: 
  • Methanotrophs consume methane as their major carbon source and have an essential role in the global carbon cycle by limiting escape of this greenhouse gas to the atmosphere. These bacteria oxidize methane to methanol by soluble and particulate methan ...

    Methanotrophs consume methane as their major carbon source and have an essential role in the global carbon cycle by limiting escape of this greenhouse gas to the atmosphere. These bacteria oxidize methane to methanol by soluble and particulate methane monooxygenases (MMOs). Soluble MMO contains three protein components, a 251-kilodalton hydroxylase (MMOH), a 38.6-kilodalton reductase (MMOR), and a 15.9-kilodalton regulatory protein (MMOB), required to couple electron consumption with substrate hydroxylation at the catalytic diiron centre of MMOH. Until now, the role of MMOB has remained ambiguous owing to a lack of atomic-level information about the MMOH-MMOB (hereafter termed H-B) complex. Here we remedy this deficiency by providing a crystal structure of H-B, which reveals the manner by which MMOB controls the conformation of residues in MMOH crucial for substrate access to the active site. MMOB docks at the α(2)β(2) interface of α(2)β(2)γ(2) MMOH, and triggers simultaneous conformational changes in the α-subunit that modulate oxygen and methane access as well as proton delivery to the diiron centre. Without such careful control by MMOB of these substrate routes to the diiron active site, the enzyme operates as an NADH oxidase rather than a monooxygenase. Biological catalysis involving small substrates is often accomplished in nature by large proteins and protein complexes. The structure presented in this work provides an elegant example of this principle.


    Organizational Affiliation

    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 beta chain
B, G, L, Q
389Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)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: 2
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase component A alpha chain
A, F, K, P
527Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)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: 3
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase component A gamma chain
C, H, M, R
170Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Gene Names: mmoZ
EC: 1.14.13.25
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P11987
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Methane monooxygenase regulatory protein B
D, I, N, S
141Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Gene Names: mmoB
Find proteins for P18797 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P18797
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, F, K, P
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.902 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 183.590α = 90.00
b = 248.970β = 90.00
c = 122.290γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references