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PDBsum entry 1vf8

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protein links
Immune system PDB id
1vf8
Jmol
Contents
Protein chain
373 a.a. *
Waters ×528
* Residue conservation analysis
PDB id:
1vf8
Name: Immune system
Title: The crystal structure of ym1 at 1.31 a resolution
Structure: Secretory protein. Chain: a. Synonym: ym1
Source: Mus musculus. House mouse. Organism_taxid: 10090
Resolution:
1.31Å     R-factor:   0.175     R-free:   0.197
Authors: S.H.Liaw,M.L.Tsai,N.C.Chang
Key ref: M.L.Tsai et al. (2004). The crystal structure of Ym1 at 1.31 A resolution. J Struct Biol, 148, 290-296. PubMed id: 15522777 DOI: 10.1016/j.jsb.2004.07.002
Date:
09-Apr-04     Release date:   15-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O35744  (CH3L3_MOUSE) -  Chitinase-like protein 3
Seq:
Struc:
398 a.a.
373 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.52  - Beta-N-acetylhexosaminidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   7 terms 
  Biological process     metabolic process   6 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
DOI no: 10.1016/j.jsb.2004.07.002 J Struct Biol 148:290-296 (2004)
PubMed id: 15522777  
 
 
The crystal structure of Ym1 at 1.31 A resolution.
M.L.Tsai, S.H.Liaw, N.C.Chang.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19307719 P.Sharma, N.Singh, M.Sinha, S.Sharma, M.Perbandt, C.Betzel, P.Kaur, A.Srinivasan, and T.P.Singh (2009).
Tryptophan as a three-way switch in regulating the function of the secretory signalling glycoprotein (SPS-40) from mammary glands: structure of SPS-40 complexed with 2-methylpentane-2,4-diol at 1.6 A resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 375-378.
PDB code: 2pi6
18329106 K.Maresz, E.D.Ponomarev, N.Barteneva, Y.Tan, M.K.Mann, and B.N.Dittel (2008).
IL-13 induces the expression of the alternative activation marker Ym1 in a subset of testicular macrophages.
  J Reprod Immunol, 78, 140-148.  
  17401190 A.S.Ethayathulla, D.B.Srivastava, J.Kumar, K.Saravanan, S.Bilgrami, S.Sharma, P.Kaur, A.Srinivasan, and T.P.Singh (2007).
Structure of the buffalo secretory signalling glycoprotein at 2.8 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 258-265.
PDB code: 2o9o
17594485 J.D.Funkhouser, and N.N.Aronson (2007).
Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family.
  BMC Evol Biol, 7, 96.  
17724034 J.Fort, L.R.de la Ballina, H.E.Burghardt, C.Ferrer-Costa, J.Turnay, C.Ferrer-Orta, I.Usón, A.Zorzano, J.Fernández-Recio, M.Orozco, M.A.Lizarbe, I.Fita, and M.Palacín (2007).
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
  J Biol Chem, 282, 31444-31452.
PDB codes: 2dh2 2dh3
17372347 J.Kumar, A.S.Ethayathulla, D.B.Srivastava, N.Singh, S.Sharma, P.Kaur, A.Srinivasan, and T.P.Singh (2007).
Carbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides.
  Acta Crystallogr D Biol Crystallogr, 63, 437-446.
PDB codes: 2dsz 2dt0 2dt1 2dt2 2dt3
16984263 H.HogenEsch, A.Dunham, R.Seymour, M.Renninger, and J.P.Sundberg (2006).
Expression of chitinase-like proteins in the skin of chronic proliferative dermatitis (cpdm/cpdm) mice.
  Exp Dermatol, 15, 808-814.  
16929095 J.Kumar, A.S.Ethayathulla, D.B.Srivastava, S.Sharma, S.B.Singh, A.Srinivasan, M.P.Yadav, and T.P.Singh (2006).
Structure of a bovine secretory signalling glycoprotein (SPC-40) at 2.1 Angstrom resolution.
  Acta Crystallogr D Biol Crystallogr, 62, 953-963.
PDB code: 2esc
  17082650 K.J.Greenlee, D.B.Corry, D.A.Engler, R.K.Matsunami, P.Tessier, R.G.Cook, Z.Werb, and F.Kheradmand (2006).
Proteomic identification of in vivo substrates for matrix metalloproteinases 2 and 9 reveals a mechanism for resolution of inflammation.
  J Immunol, 177, 7312-7321.  
16234240 A.D.Recklies, H.Ling, C.White, and S.M.Bernier (2005).
Inflammatory cytokines induce production of CHI3L1 by articular chondrocytes.
  J Biol Chem, 280, 41213-41221.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.