7M8Q | pdb_00007m8q

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7M8Q

This is version 1.1 of the entry. See complete history

Literature

Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR.

Jones, J.C.Banerjee, R.Shi, K.Semonis, M.M.Aihara, H.Pomerantz, W.C.K.Lipscomb, J.D.

(2021) Biochemistry 60: 1995-2010

  • DOI: https://doi.org/10.1021/acs.biochem.1c00293
  • Primary Citation Related Structures: 
    7M8Q, 7M8R

  • PubMed Abstract: 

    Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O 2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19 F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19 F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar K D values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.

Macromolecule Content 

  • Total Structure Weight: 277.24 kDa 
  • Atom Count: 21,830 
  • Modeled Residue Count: 2,414 
  • Deposited Residue Count: 2,424 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methane monooxygenase component A alpha chain
A, E
515Methylosinus trichosporium OB3bMutation(s): 0 
Gene Names: CQW49_12480
EC: 1.14.13.25
UniProt
Find proteins for P27353 (Methylosinus trichosporium)
Explore P27353 
Go to UniProtKB:  P27353
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27353
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Methane monooxygenase beta chain
B, F
392Methylosinus trichosporium OB3bMutation(s): 0 
Gene Names: CQW49_12475
UniProt
Find proteins for A0A2D2D5X7 (Methylosinus trichosporium (strain ATCC 35070 / NCIMB 11131 / UNIQEM 75 / OB3b))
Explore A0A2D2D5X7 
Go to UniProtKB:  A0A2D2D5X7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2D5X7
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Methane monooxygenase gamma chain
C, G
168Methylosinus trichosporium OB3bMutation(s): 0 
Gene Names: CQW49_12465
UniProt
Find proteins for A0A2D2D0T0 (Methylosinus trichosporium (strain ATCC 35070 / NCIMB 11131 / UNIQEM 75 / OB3b))
Explore A0A2D2D0T0 
Go to UniProtKB:  A0A2D2D0T0
Entity Groups
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UniProt GroupA0A2D2D0T0
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Methane monooxygenase regulatory protein B
D, H
137Methylosinus trichosporium OB3bMutation(s): 0 
Gene Names: CQW49_12470
UniProt
Find proteins for P27356 (Methylosinus trichosporium)
Explore P27356 
Go to UniProtKB:  P27356
Entity Groups
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UniProt GroupP27356
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BEZ

Query on BEZ



Download:Ideal Coordinates CCD File
K [auth A],
T [auth E]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth B]
O [auth B]
P [auth B]
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
U [auth E],
V [auth E],
X [auth F],
Y [auth G],
Z [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
R [auth E],
S [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
W [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FTR
Query on FTR
D, H
L-PEPTIDE LINKINGC11 H11 F N2 O2TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.493α = 90
b = 105.623β = 90
c = 299.704γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118030
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM08347

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description