Folate Induced Conformational Change for Methyl Transfer

Literature Report: Folate
Induced Conformational
Change for Methyl Transfer
Speaker: Chen-Yang ZHOU
Supervisor: Yun-Dong WU
Google’s home page in 5.12: Dorothy Mary Hodgkin
Dorothy Mary Hodgkin,
born in May 12, 1910
The 3rd woman to win the Nobel Prize in
Chemistry (1964), for confirmation of the
structure of penicillin and the Vitamin B12
using X-ray crystallography
What is metalloprotein
Metal + Protein = Metalloprotein
Protein containing a metal ion cofactor.
Estimated that ~ 1/2 of all proteins contain a metal.
• Example of 2 important reactions that
matalloproteins play a central role
• The advantage of metals
• 1 detailed example: the importance of protein
Example 1: Photosynthesis
6CO2 + 12 H2O
Oxygen evolution: 2H2O
C6H12O6 + 6O2 +6H2O
4e- + 4H+ + O2
• Photosynthesis is the most important reaction in our planet
• CO2 is converted into sugar, and generate O2
• Photosynthesis fixes ~1011 tons of carbon per year
• Oxygen evolution step is first key step, with metallo-oxo cluster as catalytic
• Metallo-oxo cluster
comprising 4 Mnn+ (n from 3
to 5) and 1 Ca
• Structure is controversial
• Cubane like, 2011, 1.9Å
Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen & Nobuo Kamiya. Nature 2011; 473: 55-60
Example 2: N2 Fixation
Nitrogen fixation: N2 the atmosphere is converted into ammonia NH3
In industry: Haber-Bosch Process, high temperature and pressure
In Nature: Nitrogenase
1.16Å structure resolved in 2002, but identification to the atom in the
center is still uncertain. (until 2009)
MoFeS-containing cofactor:
breaking the N,N triple bond
Einsle O, Tezcan FA, Andrade SLA, Schmid B, Yoshida M, et al. 2002. Science 297:1696–700
What’s the advantage of metals
• Metallocofactors can bind gases
• Transition metals accept lone pair that act Lewis Acids
• Form coordination complex
Red blood cell
What’s the advantage of metals
• Metallocofactors can act as supernucleophiles
SN2 reaction mechanism
Cob(I)alamin(vitamin B12):
What’s the advantage of metals
• Radical-based reaction: biotin synthase
Dethiol biotin
• Radical-based reaction: halogenation by SyrB2
Blasiak, L. C., Vaillancourt, F. H., Walsh, C. T. and Drennan, C. L. Nature 2006, 440, 368–371
We’ve seen metal play a central role,
why protein is necessary?
Detailed Example: Acetogenesis
• Carbon Fixation Without Oxygen
• Acetogenesis fixes ~1010 tons of carbon per year,
10% of total
• One of the six known pathways for carbon fixation
(Wood-Ljungdahl pathway)
• Energy efficient: lowst net ATP requirement
• O2-sensitive: Fe-S, Ni-Fe-S clusters (anaerobic)
Acetogenesis: Wood-Ljungdahl pathway
Metallo-centers in Acetogenesis
• Key to acetogenesis are protein-bound NiFeS-containing and Co-containing
Binds and transfers
Binds and reduces
CO2 to CO
Assembles the
S.W. Ragsdale, E. Pierce, Biochimica et Biophysica Acta 2008; 1784: 1873–1898 (Review)
Zoom in to the Methyl Transfer Step
Vitamine B12 derivative,
Cobalamin, is a supernucleophile
They form a complex
Corrinoid FeS
Protein Structures in Methyl Transfer Step
Why such an elaborate protein
framework (140kDa) is required
for such a simple, yet biologically
essential reaction?
Ando N, Kung Y, Can M, Bender G, Ragsdale SW, Drennan CL. (2012) J. Am. Chem. Soc. 134 (43) 17945–17954.
Protein Structures in Methyl Transfer Step
The distance for the
reactant is ~25Å
Swinging move ~7Å
towards the CH3
1. B12 must be uncapped to do
SN2 substitution, and move a
distance of ~18Å
2. Is the crystal structure active?
Is the Crystal active?
Different valance state of
Co has different color
control group
Kung Y, et al. 2012. Nature 484:265–269.
Result of ultraviolet–
visible absorption
Folate induce clamping motion: ~17Å
Resolution of crystal structures
Folate-free: 2.38 Å
Folate-bound: 3.50 Å
Kung Y, et al. 2012. Nature 484:265–269.
The last move of B12
Intriguingly, a large, continuous
electron density peak is present
in 2Fo − Fc, Fo − Fc, and
composite omit maps,
emanating from the corrin ring
and stretching directly over the
folate-binding site,
2Fo-Fc map in blue mesh (1.0 σ)
Fo-Fc difference map in green mesh (3.0 σ)
Anomalous difference map in pink mesh (4.0 σ)
Cartoon model of B12-dependent methyl transfer in
Kung Y, et al. 2012. Nature 484:265–269.
• Protein protect the reactive B12 by capping domain
before and after CH3 transfer
• The conformational change is controlled by protein,
which send the B12 to the CH3-H4folate.
• The crystal complex is active, and the conformational
change can happen even in the crystal lattice. (The
largest conformational change observed in crystal.)
• Protein scaffold and metallo center depend on each
other to have amazing reactivity and selectivity
Thank you!

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