1vf8
From Proteopedia
(New page: 200px<br /><applet load="1vf8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vf8, resolution 1.31Å" /> '''The Crystal Structur...) |
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| - | [[Image:1vf8.gif|left|200px]]<br /><applet load="1vf8" size=" | + | [[Image:1vf8.gif|left|200px]]<br /><applet load="1vf8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vf8, resolution 1.31Å" /> | caption="1vf8, resolution 1.31Å" /> | ||
'''The Crystal Structure of Ym1 at 1.31 A Resolution'''<br /> | '''The Crystal Structure of Ym1 at 1.31 A Resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Upon nematode infection, murine peritoneal macrophages synthesize and | + | Upon nematode infection, murine peritoneal macrophages synthesize and secrete large amounts of the Ym1 protein, which is a unique functional marker for alternatively activated macrophages in T(H)2-mediated inflammatory responses. Ym1 shares significant structural similarity to the family 18 chitinases. Previously, Ym1 has been studied with respect to its carbohydrate-binding ability and glycosyl hydrolysis activity and this has led to various inconclusive interpretations. Our present co-crystallization and soaking experiments with various glucosamine or N-acetylglucosamine oligomers yield only the uncomplexed Ym1. The refined Ym1 structure at 1.31A resolution clearly displays a water cluster forming an extensive hydrogen bond network with the "active-site" residues. This water cluster contributes notable electron density to lower resolution maps and this might have misled and given rise to a previous proposal for a monoglucosamine-binding site for Ym1. A structural comparison of family 18 glycosidase (-like) proteins reveals a lack of several conserved residues in Ym1, and illustrates the versatility of the divergent active sites. Therefore, Ym1 may lack N-acetylglucosamine-binding affinity, and this suggests that a new direction should be taken to unravel the function of Ym1. |
==About this Structure== | ==About this Structure== | ||
| - | 1VF8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http:// | + | 1VF8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VF8 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Chang, N | + | [[Category: Chang, N C.]] |
| - | [[Category: Liaw, S | + | [[Category: Liaw, S H.]] |
| - | [[Category: Tsai, M | + | [[Category: Tsai, M L.]] |
[[Category: chi-lectin]] | [[Category: chi-lectin]] | ||
[[Category: chitinase]] | [[Category: chitinase]] | ||
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[[Category: ym1]] | [[Category: ym1]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:34:38 2008'' |
Revision as of 13:34, 21 February 2008
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The Crystal Structure of Ym1 at 1.31 A Resolution
Overview
Upon nematode infection, murine peritoneal macrophages synthesize and secrete large amounts of the Ym1 protein, which is a unique functional marker for alternatively activated macrophages in T(H)2-mediated inflammatory responses. Ym1 shares significant structural similarity to the family 18 chitinases. Previously, Ym1 has been studied with respect to its carbohydrate-binding ability and glycosyl hydrolysis activity and this has led to various inconclusive interpretations. Our present co-crystallization and soaking experiments with various glucosamine or N-acetylglucosamine oligomers yield only the uncomplexed Ym1. The refined Ym1 structure at 1.31A resolution clearly displays a water cluster forming an extensive hydrogen bond network with the "active-site" residues. This water cluster contributes notable electron density to lower resolution maps and this might have misled and given rise to a previous proposal for a monoglucosamine-binding site for Ym1. A structural comparison of family 18 glycosidase (-like) proteins reveals a lack of several conserved residues in Ym1, and illustrates the versatility of the divergent active sites. Therefore, Ym1 may lack N-acetylglucosamine-binding affinity, and this suggests that a new direction should be taken to unravel the function of Ym1.
About this Structure
1VF8 is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.
Reference
The crystal structure of Ym1 at 1.31 A resolution., Tsai ML, Liaw SH, Chang NC, J Struct Biol. 2004 Dec;148(3):290-6. PMID:15522777
Page seeded by OCA on Thu Feb 21 15:34:38 2008
