1FYZ

METHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

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This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.

Whittington, D.A., Lippard, S.J.

(2001) J.Am.Chem.Soc. 123: 827-838

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have ...

    The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.

    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, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2
Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.270α = 90.00
b = 171.660β = 90.00
c = 221.600γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance