[phenixbb] Fucose alpha linkage

Engin Özkan eozkan at stanford.edu
Tue Nov 29 16:06:17 PST 2011


Dear Nigel and others,

I had reported a while ago that the phenix ALPHA1-3 linkage will convert 
the a-L-fucose to have a beta anomer. Actually, it was even worse; at 
the time the monomer library had the beta-L-fucose under the FUC-a-L entry.

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg13968.html
At the time, I had even created a flickr site to show the problem:
http://www.flickr.com/photos/46544052@N03/4274285327/

It has been a while since I thought about this, but I think that this 
happens specifically with L-Fucose (all other standard N-linked sugars, 
I believe they are D-sugars, are fine). Since this was not resolved at 
the time, I have resorted to this workaround:

Use your own FUC.cif, where you are sure that the C1 chiral center is alpha.
Use BETA1-3, BETA1-6 linkages to enforce alpha linkages.

I hope my memory is serving me right on this.

Since then, CNS 1.3 has incorporated the correct linkages. Please see 
the carbohydrate.top file in your CNS installation. There, on top of A13 
and A16, there are separate A13L and A16L linkages for FUC (I guess L 
stands for L-sugars, which applies only to Fucose). I would really love 
to see this corrected in Phenix and CCP4 monomer libraries (if it has 
already been fixed, thank you!).

Cheers,
Engin

P.S. Here is how CNS 1.3 does N-linked linkages:

REMARKS B1N: N-linked glycan beta link from NAG and NDG to ASN (asparagine)
!            note: PDB files with unusual NDG to ASN links are likely 
incorrect assignments
!            they will be forced into the beta anomer by the B1N link.

REMARKS B12: beta(1,2)  link from BGC, GAL, BMA, NAG, FCB, XYP to any
REMARKS B14: beta(1,4)  link from BGC, GAL, BMA, NAG, FCB, XYP to any
REMARKS A12: alpha(1,2) link from GLC, GLA, MAN, NDG, A2G, FCA to any
REMARKS A13: alpha(1,3) link from GLC, GLA, MAN, NDG, A2G, FCA to any
REMARKS A14: alpha(1,4) link from GLC, GLA, MAN, NDG, A2G, FCA to any
REMARKS A16: alpha(1,6) link from GLC, GLA, MAN, NDG, A2G, FCA to any

REMARKS B12L: beta(1,2)  link from FUL to any
REMARKS B14L: beta(1,4)  link from FUL to any
REMARKS A12L: alpha(1,2) link from FUC to any
REMARKS A13L: alpha(1,3) link from FUC to any
REMARKS A14L: alpha(1,4) link from FUC to any
REMARKS A16L: alpha(1,6) link from FUC to any

REMARKS A23: alpha(2,3) link from GAL to SIA
REMARKS A26: alpha(2,6) link from GAL to SIA

On 11/29/11 3:30 PM, Nigel Moriarty wrote:
> Tim
>
> The glycosidic bonds in PHENIX are taken from the Monomer Lib so I
> think that should be OK.
>
> O1 can be in the axial or equatorial position depending on the ring
> pucker but the O1 should always be on the opposite side of the ring
> (if you imagine the ring is flattened) from the C6. It is the
> chirality around the C1 atom that specifies the alpha/beta linkage.
> Please send me the PDB file (off-line) so I can double-check that it
> is correct. Just the three carbohydrate residues would be fine.
>
> Cheers
>
> Nigel
>
> On Tue, Nov 29, 2011 at 3:13 PM, Timothy Springer
> <springer at idi.harvard.edu>  wrote:
>> Hi, I have just added alpha1-3 and alpha1-6 fucoses to NAG. The Fucose in
>> the monomer library has O1 in the alpha position, which is axial. However,
>> after refinement, the fucose moves so it is linked beta in the equatorial
>> position.  I believe the alpha and beta linkages for Fucose may be reversed
>> in Phenix.  Please advise.
>> The links are below.
>>
>>
>>
>>
>>
>>     apply_cif_link {
>>       data_link = "ALPHA1-3"
>>       residue_selection_1 = "chain A and resname NAG and resid 3821"
>>       residue_selection_2 = "chain A and resname FUC and resid 3824"
>>     }
>>     apply_cif_link {
>>       data_link = "ALPHA1-6"
>>       residue_selection_1 = "chain A and resname NAG and resid 3821"
>>       residue_selection_2 = "chain A and resname FUC and resid 3823"
>>     }
>>
>>
>> With my best regards,
>> Tim
>> Timothy A. Springer, Ph.D.
>> Latham Family Professor of Biological Chemistry and Molecular Pharmacology
>>
>> Harvard Medical School                   http://idi.harvard.edu/springer
>> Immune Disease Institute                 springer at idi.harvard.edu
>> Program in Cellular and Molecular Medicine, Dept. Medicine
>> Div. Hematology                                 Children's Hospital Boston
>> 3 Blackfan Circle, Rm 3103              phone:  617-713-8200
>> Boston MA 02115                               fax:        617-713-8232
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>


-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111



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