7M8R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
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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)
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Entity Groups  
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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 OB3b)
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UniProt GroupA0A2D2D5X7
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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 OB3b)
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UniProt GroupA0A2D2D0T0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase regulatory protein B
D, H
136Methylosinus trichosporium OB3bMutation(s): 1 
Gene Names: CQW49_12470
UniProt
Find proteins for P27356 (Methylosinus trichosporium)
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UniProt GroupP27356
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
KA [auth E],
O [auth A]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
W6X
Query on W6X

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CB [auth H],
DA [auth D]
1,1,1-tris(fluoranyl)propan-2-one
C3 H3 F3 O
FHUDAMLDXFJHJE-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth G]
BA [auth C]
BB [auth H]
CA [auth D]
AA [auth C],
AB [auth G],
BA [auth C],
BB [auth H],
CA [auth D],
HA [auth E],
IA [auth E],
JA [auth E],
K [auth A],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
OA [auth E],
P [auth A],
PA [auth F],
Q [auth A],
QA [auth F],
R [auth A],
RA [auth F],
S [auth A],
SA [auth F],
T [auth A],
TA [auth F],
U [auth A],
UA [auth F],
V [auth B],
VA [auth F],
W [auth B],
WA [auth F],
X [auth B],
XA [auth F],
Y [auth B],
YA [auth G],
Z [auth B],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

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FA [auth E],
GA [auth E],
I [auth A],
J [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 2.22 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.388α = 90
b = 105.466β = 90
c = 298.184γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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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