Dear Colleagues,

The amidine originating from the condensation reaction between the 
Met N-formyl group and the His side chain should be the other way 
around! This would also be roughly consistent with the reported 
geometry. In fact, there should be two mesomeric states, provided 
there is N protonation.

Arne Skerra



At 5:56 Uhr -0400 10.10.2008, Artem Evdokimov wrote:
>If you're 100% sure that this is only one atom then amination comes to mind.
>I have no clue what conditions would favor such reactivity but it is
>possible that the formyl group on the Met was aminated with the cyclic N of
>the histidine, resulting in either a substituted bis-amine (requires
>reduction, may not be stable) or in a cyclic amidine (the latter requires
>four atoms - N1-C=N-Ca - to be in the same plane). This amidine should have
>some pretty interesting properties (probably more like a Schiff base than an
>amidine).
>
>Could you tell us a bit more about the system you're working with?
>
>Artem
>
>P.S. The bond lengths you describe are not typical for C-N, however at 1.9A
>resolution it is not very likely that the values you measured actually
>correspond to the bond lengths (hopefully, because otherwise you have
>
>-----Original Message-----
>From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>gerwald jogl
>Sent: Thursday, October 09, 2008 4:24 PM
>To: [log in to unmask]
>Subject: [ccp4bb] Potential N-terminal cyclization
>
>Hi All,
>
>I am looking for some input regarding an unusual feature in one of our
>structures. Maybe someone has come across something similar or has some
>thoughts about it...
>
>We have a 1.9 A crystal structure with well-defined density in the
>N-terminal region. The side chain of His3 is oriented towards the
>N-terminal amino group of Met1 and there is a nice difference density
>'ball' right in between the His and the amino group suggesting that
>there is an additional atom that is covalently linked. There are two
>molecules in the asu and both show the same feature (no ncs refinement).
>My problem is that I cannot come up with a reaction that would result in
>such a linkage and there is not much to be found in the literature.
>
>If I place a hypothetical atom in the difference density peak, I can
>measure distances and angles. Here are some numbers: Distance from atom
>X to the N-terminal nitrogen 1.72 (1.64 in chain B). Distance from atom
>X to His NE2 1.58 (1.45 in chain B; the temperature factors of the His
>side chain are slightly more consistent with this ring orientation
>compared to the 180 degree flip that would bring CE1 towards atom X).
>Atom X is coplanar with the His ring. The angle between NE2 - X - N1 is
>95 deg (106 in chain B). The angle between X - N1 - Calpha1 is 111
>degrees in both chains. As the N-terminal methionine is still present,
>it is possible that the methionine formyl-group was present before the
>hypothetical reaction. However, there is only one 'atom' in the
>difference density.
>
>Any comments or suggestions would be highly welcome.
>Gerwald


-- 

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Prof. Dr. Arne Skerra                                  [log in to unmask]
Lehrstuhl f. Biologische Chemie               Phone: +49 (0)8161 71-4351
Technische Universitaet Muenchen                Fax:               -4352
85350 Freising-Weihenstephan
Germany                                         http://www.wzw.tum.de/bc
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