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O35744 (CHIL3_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Chitinase-like protein 3

EC=3.2.1.52
Alternative name(s):
Beta-N-acetylhexosaminidase Ym1
Chitinase-3-like protein 3
ECF-L
Eosinophil chemotactic cytokine
Secreted protein Ym1
Gene names
Name:Chil3
Synonyms:Chi3l3, Ym1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length398 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.2 Ref.3 Ref.7

Catalytic activity

Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. Ref.7

Subcellular location

Secreted. Rough endoplasmic reticulum lumen. Nucleus envelope. Cytoplasm. Cytoplasmic granule. Note: Predominantly localizes to the lumen of rough endoplasmic reticulum (rER) and nuclear envelope in alveolar macrophages. Localizes to the dilated lumen of rER in immature neutrophils in spleen and in cytoplasmic granules in peritoneal neutrophils. Detected in needle-shaped crystals present in the cytoplasm of bone marrow macrophages. Ref.3 Ref.7 Ref.10

Tissue specificity

Expressed in peritoneal cavity macrophages and in peritoneal and bone marrow-derived neutrophils. Abundantly expressed in bone marrow, with moderate levels detected in gastric antrum, spleen and in alveolar macrophages in lung. Not detected in brain, heart, liver, kidney, stomach, intestine, skeletal muscle, ovary, testis, thymus and lymph nodes (at protein level). Detected at low levels in bone marrow, spleen, thymus and lung. Barely detectable in intestine, kidney and coecum. Ref.1 Ref.2 Ref.3 Ref.7 Ref.9 Ref.10

Developmental stage

In yolk sac, first detected at low levels at E8.5, with significant expression detected at E10.5 in myeloid precursor cells. In liver, expressed from E16.5 to P7.5 with highest levels detected from E18.5 to P0.5. In spleen, first detected at E16.5, with peak levels detected at E18.5 and P0.5 and expression persisting through the spleen maturation to the adult stage. In bone marrow, high expression levels detected from E16.5 until adulthood. In lung, first detected around the time of birth, with levels increasing significantly from P14.5 towards adulthood. Ref.9

Induction

Up-regulated in response to IL3 and IL4, during the inflammatory response and upon parasitic infection. Ref.2 Ref.3 Ref.8 Ref.9

Sequence similarities

Belongs to the glycosyl hydrolase 18 family. Chitinase class II subfamily.

Biophysicochemical properties

Kinetic parameters:

4-methylumbelliferone-N-acetylglucosamine (MU-(GlcNAc)1) is a GlcNAc2 analog.

KM=120.8 µM for 4-methylumbelliferone-N-acetylglucosamine (at pH 4-4.5) Ref.7

Vmax=0.023 µmol/min/mg enzyme

pH dependence:

Optimum pH is 4.5-5.0.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2121 Ref.2 Ref.3
Chain22 – 398377Chitinase-like protein 3
PRO_0000011970

Sites

Binding site1401Chitooligosaccharide Probable
Binding site2131Chitooligosaccharide Probable

Amino acid modifications

Disulfide bond26 ↔ 51 Ref.11 Ref.12
Disulfide bond49 ↔ 394 Ref.11 Ref.12
Disulfide bond307 ↔ 372 Ref.11 Ref.12

Experimental info

Sequence conflict1051P → S no nucleotide entry Ref.1
Sequence conflict1051P → S in BAA13458. Ref.2
Sequence conflict2571S → P in BAE23385. Ref.3
Sequence conflict3611P → R no nucleotide entry Ref.1

Secondary structure

....................................................................... 398
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O35744 [UniParc].

Last modified March 1, 2001. Version 2.
Checksum: C11187661B99D1D1

FASTA39844,458
        10         20         30         40         50         60 
MAKLILVTGL AILLNVQLGS SYQLMCYYTS WAKDRPIEGS FKPGNIDPCL CTHLIYAFAG 

        70         80         90        100        110        120 
MQNNEITYTH EQDLRDYEAL NGLKDKNTEL KTLLAIGGWK FGPAPFSAMV STPQNRQIFI 

       130        140        150        160        170        180 
QSVIRFLRQY NFDGLNLDWQ YPGSRGSPPK DKHLFSVLVK EMRKAFEEES VEKDIPRLLL 

       190        200        210        220        230        240 
TSTGAGIIDV IKSGYKIPEL SQSLDYIQVM TYDLHDPKDG YTGENSPLYK SPYDIGKSAD 

       250        260        270        280        290        300 
LNVDSIISYW KDHGAASEKL IVGFPAYGHT FILSDPSKTG IGAPTISTGP PGKYTDESGL 

       310        320        330        340        350        360 
LAYYEVCTFL NEGATEVWDA PQEVPYAYQG NEWVGYDNVR SFKLKAQWLK DNNLGGAVVW 

       370        380        390 
PLDMDDFSGS FCHQRHFPLT STLKGDLNIH SASCKGPY 

« Hide

References

« Hide 'large scale' references
[1]"Genetic characterization of the murine Ym1 gene and identification of a cluster of highly homologous genes."
Jin H.M., Copeland N.G., Gilbert D.J., Jenkins N.A., Kirkpatrick R.B., Rosenberg M.
Genomics 54:316-322(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY.
Strain: 129/SvJ.
[2]"Identification of a novel eosinophil chemotactic cytokine (ECF-L) as a chitinase family protein."
Owhashi M., Arita H., Hayai N.
J. Biol. Chem. 275:1279-1286(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 22-39, FUNCTION, TISSUE SPECIFICITY, INDUCTION.
Tissue: Bone marrow.
[3]"A macrophage protein, Ym1, transiently expressed during inflammation is a novel mammalian lectin."
Chang N.-C.A., Hung S.-I., Hwa K.-Y., Kato I., Chen J.-E., Liu C.-H., Chang A.C.
J. Biol. Chem. 276:17497-17506(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 22-48; 109-134; 162-192 AND 210-225, FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
Tissue: Macrophage.
[4]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: NOD.
Tissue: Bone and Dendritic cell.
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Heart and Lung.
[6]"Mouse chitinase-related protein mRNA (MCRP), partial cds."
Shmelkov S.V., Zinovjeva M.V., Belyavsky A.V.
Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 139-398.
Strain: CBA.
Tissue: Bone marrow.
[7]"Ym1 is a neutrophil granule protein that crystallizes in p47phox-deficient mice."
Harbord M., Novelli M., Canas B., Power D., Davis C., Godovac-Zimmermann J., Roes J., Segal A.W.
J. Biol. Chem. 277:5468-5475(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[8]"TH2 cytokines and allergic challenge induce Ym1 expression in macrophages by a STAT6-dependent mechanism."
Welch J.S., Escoubet-Lozach L., Sykes D.B., Liddiard K., Greaves D.R., Glass C.K.
J. Biol. Chem. 277:42821-42829(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION BY IL3 AND IL4.
[9]"Transient expression of Ym1, a heparin-binding lectin, during developmental hematopoiesis and inflammation."
Hung S.I., Chang A.C., Kato I., Chang N.C.
J. Leukoc. Biol. 72:72-82(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
[10]"Cellular expression of murine Ym1 and Ym2, chitinase family proteins, as revealed by in situ hybridization and immunohistochemistry."
Nio J., Fujimoto W., Konno A., Kon Y., Owhashi M., Iwanaga T.
Histochem. Cell Biol. 121:473-482(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[11]"The crystal structure of a novel mammalian lectin, Ym1, suggests a saccharide binding site."
Sun Y.-J., Chang N.-C.A., Hung S.-I., Chang A.C., Chou C.-C., Hsiao C.-D.
J. Biol. Chem. 276:17507-17514(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 22-398, DISULFIDE BONDS.
[12]"The crystal structure of Ym1 at 1.31 A resolution."
Tsai M.L., Liaw S.H., Chang N.C.
J. Struct. Biol. 148:290-296(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.31 ANGSTROMS) OF 22-398, DISULFIDE BONDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D87757 mRNA. Translation: BAA13458.2.
M94584 mRNA. Translation: AAB62394.2.
AK137503 mRNA. Translation: BAE23385.1.
AK154420 mRNA. Translation: BAE32572.1.
BC061154 mRNA. Translation: AAH61154.1.
U56900 mRNA. Translation: AAB01230.1.
CCDSCCDS17718.1.
PIRS27879.
RefSeqNP_034022.2. NM_009892.2.
UniGeneMm.387173.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1E9LX-ray2.50A22-398[»]
1VF8X-ray1.31A22-398[»]
ProteinModelPortalO35744.
SMRO35744. Positions 22-394.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO35744. 1 interaction.
MINTMINT-4090737.

Chemistry

ChEMBLCHEMBL1795141.

Protein family/group databases

CAZyGH18. Glycoside Hydrolase Family 18.

Proteomic databases

MaxQBO35744.
PaxDbO35744.
PRIDEO35744.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000063062; ENSMUSP00000053923; ENSMUSG00000040809.
GeneID12655.
KEGGmmu:12655.
UCSCuc008qvw.2. mouse.

Organism-specific databases

CTD12655.
MGIMGI:1330860. Chil3.

Phylogenomic databases

eggNOGCOG3325.
GeneTreeENSGT00550000074323.
HOGENOMHOG000111109.
HOVERGENHBG011684.
InParanoidO35744.
KOK17524.
OMAIISYWKD.
OrthoDBEOG7ZGX3G.
PhylomeDBO35744.
TreeFamTF315610.

Gene expression databases

ArrayExpressO35744.
BgeeO35744.
CleanExMM_CHI3L3.
GenevestigatorO35744.

Family and domain databases

Gene3D3.10.50.10. 1 hit.
3.20.20.80. 2 hits.
InterProIPR011583. Chitinase_II.
IPR029070. Chitinase_insertion.
IPR001223. Glyco_hydro18cat.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamPF00704. Glyco_hydro_18. 1 hit.
[Graphical view]
SMARTSM00636. Glyco_18. 1 hit.
[Graphical view]
SUPFAMSSF51445. SSF51445. 2 hits.
SSF54556. SSF54556. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO35744.
NextBio281876.
PROO35744.
SOURCESearch...

Entry information

Entry nameCHIL3_MOUSE
AccessionPrimary (citable) accession number: O35744
Secondary accession number(s): P70201 expand/collapse secondary AC list , Q3U462, Q3UV87, Q61201
Entry history
Integrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: March 1, 2001
Last modified: July 9, 2014
This is version 110 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries