Hi, Not sure what you mean by 'other way around' - the formula you drew is what I was thinking about :) Mesomeric states in normal amidines are averaged and should result in planarity - since this case does not seem to have a planar geometry, there's a chance that the amidine never formed and the transient Schiff base was reduced by something. There is also an off chance that the Histidine side chain was attacked on the *carbon* rather than the NH. This does happen and has been observed in studies dealing with heat- and aldehyde-driven crosslinking of proteins. However the image of the e.d. that I saw does not support this.
Artem > 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:[EMAIL PROTECTED] On Behalf Of >>gerwald jogl >>Sent: Thursday, October 09, 2008 4:24 PM >>To: CCP4BB@JISCMAIL.AC.UK >>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 > > > -- > > ------------------------------------------------------------------------ > Prof. Dr. Arne Skerra [EMAIL PROTECTED] > 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 > ------------------------------------------------------------------------
