[phenixbb] Glycan refinement

Engin Ozkan eozkan at stanford.edu
Tue Nov 10 11:26:14 PST 2009

This question just seems to come again and again. Search on the web with 
phenixbb and glycan or mannose, etc. You'll see the answer.

I do have a related question to the developers, however. In recent 
articles published, it was pointed out that 30% of glycoproteins in the 
pdb had incorrect geometries and names for sugars (Lutteke, Frank, von 
der Lieth, Carbohydrate Research, 2004; Crispin, Stuart, Jones, NSMB, 
2007). The most common error apparently is the alpha mannose having beta 
geometry, and vice versa. We are also told that beta mannose should have 
the three-letter code BMA, and alpha mannose is MAN, which is a nice 
convention to follow. Unfortunately, this convention is not always 
followed by users, and monomer libraries come with definitions for both 
alpha and beta anomers called the same three-letter code. The fact that 
both stereoisomers are found in the same glycosylation chain in all 
eukaryotes, actually linked to each other, makes an ugly sight. This is 
like having a polypeptide chain of L-Ala linked to D-Ala, and calling it 
Ala-Ala, which would cause confusion. Of course, if the person who 
modeled the structure knows to use the correct cif link, the 
stereochemistry is correct, but it will not be clear to people looking 
at the sequence or even at the actual structure; rules for defining 
anomers are complicated. (Just to make things worse, I don't currently 
see a BMA.cif in the phenix monomer library, although it is in the list 
file. Thankfully, there is a MAN-b-D, which one can modify to have a 
three-letter code of BMA. Or one can use the ccp4 monomer library for a 
BMA cif file).

Would the developers creating the extremely useful monomer libraries be 
interested in taking into account naming conventions for glycoproteins 
to help new users avoid confusion and possibly mistakes? There is now 
software for checking proteoglycan naming and chemistries (Lutteke, von 
der Lieth, BMC Bionformatics, 2004; Berman, Henrick, Nakamura, Markley, 
NSMB, 2007), and it would also be great incorporating these into 
validation tools that come with PHENIX, if possible. Nucleic acids and 
polypeptides might be special, but glycosylation deserves some 
attention, too, and I believe PDB now sends you warnings if you are 
trying to deposit structures with incorrectly modeled glycans.


On 11/10/09 10:12 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> Dear All,
> I am refining a structure with a N-linked glycosylation site. There is 
> density that goes beyond the first NAG, at least to MAN3. I know in 
> Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I 
> don’t know how to do the “apply_cif_link’ for the extensions such 
> NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
> Thanks,
> Tongqing
> *Tongqing Zhou, Ph.D. *
> Staff Scientist
> Structural Biology Section
> Vaccine Research Center, NIAID/NIH
> Building 40, Room 4607B
> 40 Convent Drive, MSC3027
> Bethesda, MD 20892
> (301) 594-8710 (Tel)
> (301) 793-0794 (Cell)
> (301) 480-2658 (Fax)
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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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