1XVB

soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


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:  
    1XU3, 1XU5, 1XVB, 1XVC, 1XVD, 1XVE, 1XVF, 1XVG

  • 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 is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methane monooxygenase component A alpha chainA, B527Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P22869 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P22869 
Go to UniProtKB:  P22869
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22869
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methane monooxygenase component A beta chainC, D389Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P18798 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P18798 
Go to UniProtKB:  P18798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18798
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Methane monooxygenase component A gamma chainE, F170Methylococcus capsulatusMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore P11987 
Go to UniProtKB:  P11987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11987
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BHL
Query on BHL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
T [auth B],
U [auth B],
V [auth B]
6-BROMOHEXAN-1-OL
C6 H13 Br O
FCMCSZXRVWDVAW-UHFFFAOYSA-N
 Ligand Interaction
BBU
Query on BBU

Download Ideal Coordinates CCD File 
L [auth A]1-BROMOBUTANE
C4 H9 Br
MPPPKRYCTPRNTB-UHFFFAOYSA-N
 Ligand Interaction
3BR
Query on 3BR

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X [auth C],
Y [auth C]
1-BROMOPROPANE
C3 H7 Br
CYNYIHKIEHGYOZ-UHFFFAOYSA-N
 Ligand Interaction
BBX
Query on BBX

Download Ideal Coordinates CCD File 
S [auth B]1-BROMOETHANE
C2 H5 Br
RDHPKYGYEGBMSE-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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G [auth A],
H [auth A],
O [auth B],
P [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
W [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.632α = 90
b = 171.867β = 90
c = 220.622γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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