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46  structures 1275  species 0  interactions 5306  sequences 152  architectures

Family: Glyco_hydro_19 (PF00182)

Summary: Chitinase class I

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This is the Wikipedia entry entitled "Glycoside hydrolase family 19". More...

Glycoside hydrolase family 19 Edit Wikipedia article

Glycosyl hydrolases family 19
PDB 2baa EBI.jpg
the refined crystal structure of an endochitinase from hordeum vulgare l. seeds to 1.8 angstroms resolution
Identifiers
SymbolGlyco_hydro_19
PfamPF00182
Pfam clanCL0037
InterProIPR000726
PROSITEPDOC00620
SCOP22baa / SCOPe / SUPFAM
CAZyGH19

In molecular biology, Glycoside hydrolase family 19 is a family of glycoside hydrolases.

Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families.[1][2][3] This classification is available on the CAZy(http://www.cazy.org/GH1.html) web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes. [5]

Glycoside hydrolase family 19 CAZY GH_19 comprises enzymes with only one known activity; chitinase (EC 3.2.1.14).

Chitinases[6] are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19.[7] Chitinases of family 19 (also known as classes IA or I and IB or II) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Class IA/I and IB/II enzymes differ in the presence (IA/I) or absence (IB/II) of a N-terminal chitin-binding domain. The catalytic domain of these enzymes consist of about 220 to 230 amino acid residues.

References

  1. ^ Henrissat B, Callebaut I, Mornon JP, Fabrega S, Lehn P, Davies G (1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7090–7094. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Henrissat B, Davies G (1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853–859. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
  3. ^ Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
  4. ^ Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
  5. ^ CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
  6. ^ Jolles P, Flach J, Pilet PE (1992). "What's new in chitinase research?". Experientia. 48 (8): 701–716. doi:10.1007/BF02124285. PMID 1516675.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ Henrissat B (1991). "A classification of glycosyl hydrolases based on amino acid sequence similarities". Biochem. J. 280 ( Pt 2): 309–16. PMC 1130547. PMID 1747104. {{cite journal}}: Unknown parameter |month= ignored (help)
This article incorporates text from the public domain Pfam and InterPro: IPR000726

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Chitinase class I Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000726

O-Glycosyl hydrolases ( EC ) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [ PUBMED:7624375 , PUBMED:8535779 ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 19 CAZY comprises enzymes with only one known activity; chitinase ( EC ).

Chitinases [ PUBMED:1516675 ] are enzymes that catalyse the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19 [ PUBMED:1747104 ]. Chitinases of family 19 (also known as classes I, II and IV) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Some family 19 chitinases are found in bacteria. Class I and II chitinases are similar in their catalytic domains. Class I chitinases have an N-terminal cysteine-rich, chitin-binding domain which is separated from the catalytic domain by a proline and glycine-rich hinge region. Class II chitinases lack both the chitin-binding domain and the hinge region. Class IV chitinases are similar to class I, but they are smaller in size due to certain deletions.

Despite any significant sequence homology with lysozymes, structural analysis reveals that family 19 chitinases, together with family 46 chitosanases, are similar to several lysozymes including those from T4-phage and from goose. The structures reveal that the different enzyme groups arose from a common ancestor glycohydrolase antecedent to the procaryotic/eucaryotic divergence [ PUBMED:10957628 , PUBMED:12369923 , PUBMED:10906956 , PUBMED:10906957 , PUBMED:9723170 , PUBMED:8564539 ].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Lysozyme (CL0037), which has the following description:

Barley chitinase, bacterial chitosanase, and lysozymes from phage and animals all hydrolyse related polysaccharides. The proteins little amino-acid similarity, but have a structurally invariant core consisting of two helices and a three-stranded beta-sheet which form the substrate-binding and catalytic cleft [1].

The clan contains the following 21 members:

Destabilase DUF3218 Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Glyco_hydro_80 Lys Lysozyme_like Peptidase_U40 Pesticin Phage_lysozyme Phage_lysozyme2 SLT SLT_2 SLT_3 SLT_4 TraH_2 Transgly Transglycosylas Utp11

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(6)
Full
(5306)
Representative proteomes UniProt
(17028)
RP15
(849)
RP35
(2723)
RP55
(5015)
RP75
(7457)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(6)
Full
(5306)
Representative proteomes UniProt
(17028)
RP15
(849)
RP35
(2723)
RP55
(5015)
RP75
(7457)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(6)
Full
(5306)
Representative proteomes UniProt
(17028)
RP15
(849)
RP35
(2723)
RP55
(5015)
RP75
(7457)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: chitinase_1;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 6
Number in full: 5306
Average length of the domain: 158.7 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 58.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 232
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Glyco_hydro_19 domain has been found. There are 46 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077Z915 View 3D Structure Click here
A0A077ZFP5 View 3D Structure Click here
A0A077ZLY8 View 3D Structure Click here
A0A0K0EQ39 View 3D Structure Click here
A0A0K0ET67 View 3D Structure Click here
A0A0P0XWU1 View 3D Structure Click here
A0A0R0HQE5 View 3D Structure Click here
A0A0R0HSB0 View 3D Structure Click here
A0A1D6E7B3 View 3D Structure Click here
A0A1D6GWN1 View 3D Structure Click here
A0A1D6GWN3 View 3D Structure Click here
A0A1D6JS63 View 3D Structure Click here
A0A1D6K7T5 View 3D Structure Click here
A0A1D6LKX7 View 3D Structure Click here
A0A1D6LMS1 View 3D Structure Click here
A0A1D6LMS5 View 3D Structure Click here
A0A1D6PVW4 View 3D Structure Click here
A0A1P8AME8 View 3D Structure Click here
A0A1P8AWZ7 View 3D Structure Click here
A0A1X7YIJ7 View 3D Structure Click here
B4F9D5 View 3D Structure Click here
B4FTS6 View 3D Structure Click here
B4G1H3 View 3D Structure Click here
B6TR38 View 3D Structure Click here
B6TT00 View 3D Structure Click here
C0P3M6 View 3D Structure Click here
C0P451 View 3D Structure Click here
C0PKN5 View 3D Structure Click here
C6T7J9 View 3D Structure Click here
C6TNB0 View 3D Structure Click here
F4JBK4 View 3D Structure Click here
I1J8E1 View 3D Structure Click here
I1JBA3 View 3D Structure Click here
I1KWS8 View 3D Structure Click here
I1L0T4 View 3D Structure Click here
I1M587 View 3D Structure Click here
I1MGH1 View 3D Structure Click here
I1MMY2 View 3D Structure Click here
I1N4Z6 View 3D Structure Click here
K0F7G5 View 3D Structure Click here