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1vf8

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The Crystal Structure of Ym1 at 1.31 A Resolution

Structural highlights

1vf8 is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.31Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CHIL3_MOUSE Lectin that binds saccharides with a free amino group, such as glucosamine or galactosamine. Binding to oligomeric saccharides is much stronger than binding to mono- or disaccharides. Also binds chitin and heparin. Has weak hexosaminidase activity but no chitinase activity. Has chemotactic activity for T-lymphocytes, bone marrow cells and eosinophils. May play a role in inflammation and allergy.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Owhashi M, Arita H, Hayai N. Identification of a novel eosinophil chemotactic cytokine (ECF-L) as a chitinase family protein. J Biol Chem. 2000 Jan 14;275(2):1279-86. PMID:10625674
↑ Chang NC, Hung SI, Hwa KY, Kato I, Chen JE, Liu CH, Chang AC. A macrophage protein, Ym1, transiently expressed during inflammation is a novel mammalian lectin. J Biol Chem. 2001 May 18;276(20):17497-506. Epub 2001 Jan 31. PMID:11297523 doi:http://dx.doi.org/10.1074/jbc.M010417200
↑ Harbord M, Novelli M, Canas B, Power D, Davis C, Godovac-Zimmermann J, Roes J, Segal AW. Ym1 is a neutrophil granule protein that crystallizes in p47phox-deficient mice. J Biol Chem. 2002 Feb 15;277(7):5468-75. Epub 2001 Dec 3. PMID:11733538 doi:http://dx.doi.org/10.1074/jbc.M110635200
↑ Tsai ML, Liaw SH, Chang NC. The crystal structure of Ym1 at 1.31 A resolution. J Struct Biol. 2004 Dec;148(3):290-6. PMID:15522777 doi:10.1016/j.jsb.2004.07.002

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vf8"

Categories: Large Structures | Mus musculus | Chang NC | Liaw SH | Tsai ML

@@ Line 1: / Line 1: @@
 ==The Crystal Structure of Ym1 at 1.31 A Resolution==
-<StructureSection load='1vf8' size='340' side='right' caption='[[1vf8]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
+<StructureSection load='1vf8' size='340' side='right'caption='[[1vf8]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vf8]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VF8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vf8]] is a 1 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VF8 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1e9l|1e9l]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.31&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vf8 OCA], [http://pdbe.org/1vf8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vf8 RCSB], [http://www.ebi.ac.uk/pdbsum/1vf8 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vf8 OCA], [https://pdbe.org/1vf8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vf8 RCSB], [https://www.ebi.ac.uk/pdbsum/1vf8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vf8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CHIL3_MOUSE CHIL3_MOUSE]] Lectin that binds saccharides with a free amino group, such as glucosamine or galactosamine. Binding to oligomeric saccharides is much stronger than binding to mono- or disaccharides. Also binds chitin and heparin. Has weak hexosaminidase activity but no chitinase activity. Has chemotactic activity for T-lymphocytes, bone marrow cells and eosinophils. May play a role in inflammation and allergy.<ref>PMID:10625674</ref> <ref>PMID:11297523</ref> <ref>PMID:11733538</ref>
+[https://www.uniprot.org/uniprot/CHIL3_MOUSE CHIL3_MOUSE] Lectin that binds saccharides with a free amino group, such as glucosamine or galactosamine. Binding to oligomeric saccharides is much stronger than binding to mono- or disaccharides. Also binds chitin and heparin. Has weak hexosaminidase activity but no chitinase activity. Has chemotactic activity for T-lymphocytes, bone marrow cells and eosinophils. May play a role in inflammation and allergy.<ref>PMID:10625674</ref> <ref>PMID:11297523</ref> <ref>PMID:11733538</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vf/1vf8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vf/1vf8_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vf8 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Chang, N C]]
+[[Category: Chang NC]]
-[[Category: Liaw, S H]]
+[[Category: Liaw SH]]
-[[Category: Tsai, M L]]
+[[Category: Tsai ML]]
-[[Category: Chi-lectin]]
-[[Category: Chitinase]]
-[[Category: Functional versatility]]
-[[Category: Immune system]]
-[[Category: Structural plasticity]]
-[[Category: Ym1]]

1vf8

From Proteopedia

Current revision

The Crystal Structure of Ym1 at 1.31 A Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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