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285  structures 6865  species 0  interactions 33147  sequences 573  architectures

Family: Glyco_hydro_3 (PF00933)

Summary: Glycosyl hydrolase family 3 N terminal domain

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This is the Wikipedia entry entitled "Glycoside hydrolase family 3". More...

Glycoside hydrolase family 3 Edit Wikipedia article

Glycosyl hydrolase family 3 N terminal domain
Identifiers
SymbolGlyco_hydro_3
PfamPF00933
Pfam clanCL0058
InterProIPR001764
PROSITEPDOC00621
SCOPe1ex1 / SUPFAM
CAZyGH3
Glycosyl hydrolase family 3 C-terminal domain
PDB 1ieq EBI.jpg
crystal structure of barley beta-d-glucan glucohydrolase isoenzyme exo1
Identifiers
SymbolGlyco_hydro_3_C
PfamPF01915
InterProIPR002772
PROSITEPDOC00621
SCOPe1ex1 / SUPFAM

In molecular biology, glycoside hydrolase family 3 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 web site,[4][5] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[6][7]

Glycoside hydrolase family 3 CAZY GH_3 comprises enzymes with a number of known activities; beta-glucosidase (EC 3.2.1.21); beta-xylosidase (EC 3.2.1.37); N-acetyl beta-glucosaminidase (EC 3.2.1.52); glucan beta-1,3-glucosidase (EC 3.2.1.58); cellodextrinase (EC 3.2.1.74); exo-1,3-1,4-glucanase (EC 3.2.1). These enzymes are two-domain globular proteins that are N-glycosylated at three sites.[8]

External links

References

  1. ^ Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G (July 1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proceedings of the National Academy of Sciences of the United States of America. 92 (15): 7090–4. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.
  2. ^ Davies G, Henrissat B (September 1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853–9. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
  3. ^ Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 (Pt 2): 695–6. doi:10.1042/bj3160695. PMC 1217404. PMID 8687420.
  4. ^ "Home". CAZy.org. Retrieved 2018-03-06.
  5. ^ Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (January 2014). "The carbohydrate-active enzymes database (CAZy) in 2013". Nucleic Acids Research. 42 (Database issue): D490–5. doi:10.1093/nar/gkt1178. PMC 3965031. PMID 24270786.
  6. ^ "Glycoside Hydrolase Family 3". CAZypedia.org. Retrieved 2018-03-06.
  7. ^ CAZypedia Consortium (December 2018). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes" (PDF). Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. PMID 29040563.
  8. ^ Varghese JN, Hrmova M, Fincher GB (February 1999). "Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase". Structure. 7 (2): 179–90. doi:10.1016/S0969-2126(99)80024-0. PMID 10368285.
This article incorporates text from the public domain Pfam and InterPro: IPR001764
This article incorporates text from the public domain Pfam and InterPro: IPR002772

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.

Glycosyl hydrolase family 3 N terminal domain Provide feedback

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Literature references

  1. Varghese JN, Hrmova M, Fincher GB; , Structure Fold Des 1999;7:179-190.: Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase. PUBMED:10368285 EPMC:10368285


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001764

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 3 CAZY comprises enzymes with a number of known activities; beta-glucosidase ( EC ); beta-xylosidase ( EC ); N-acetyl beta-glucosaminidase ( EC ); glucan beta-1,3-glucosidase ( EC ); cellodextrinase ( EC ); exo-1,3-1,4-glucanase ( EC ). These enzymes are two-domain globular proteins that are N-glycosylated at three sites [ PUBMED:10368285 ]. This domain is often N-terminal to the glycoside hydrolase family 3, C-terminal domain INTERPRO .

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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...

View options

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
(9)
Full
(33147)
Representative proteomes UniProt
(112201)
RP15
(3275)
RP35
(14106)
RP55
(29791)
RP75
(50391)
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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
(9)
Full
(33147)
Representative proteomes UniProt
(112201)
RP15
(3275)
RP35
(14106)
RP55
(29791)
RP75
(50391)
Alignment:
Format:
Order:
Sequence:
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Download options

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
(9)
Full
(33147)
Representative proteomes UniProt
(112201)
RP15
(3275)
RP35
(14106)
RP55
(29791)
RP75
(50391)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_1151 (release 3.0)
Previous IDs: glycosyl_hydr14;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 9
Number in full: 33147
Average length of the domain: 284.70 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 40.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.6 21.4
Noise cut-off 21.2 21.3
Model length: 319
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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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_3 domain has been found. There are 285 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
A0A0P0Y1K3 View 3D Structure Click here
A0A0P0Y573 View 3D Structure Click here
A0A0R0EWH1 View 3D Structure Click here
A0A0R0EX33 View 3D Structure Click here
A0A0R0FL35 View 3D Structure Click here
A0A0R0G057 View 3D Structure Click here
A0A0R0G057 View 3D Structure Click here
A0A0R0HT51 View 3D Structure Click here
A0A0R0JU29 View 3D Structure Click here
A0A0R0L894 View 3D Structure Click here
A0A1D6E4T8 View 3D Structure Click here
A0A1D6EGK8 View 3D Structure Click here
A0A1D6GH62 View 3D Structure Click here
A0A1D6JFG2 View 3D Structure Click here
A0A1D6L4E9 View 3D Structure Click here
A0A1D6L4F0 View 3D Structure Click here
A0A1D6M4Z2 View 3D Structure Click here
A0A1D6NAD2 View 3D Structure Click here
A0A1D6QK01 View 3D Structure Click here
A0A1D6QU17 View 3D Structure Click here
A0A1D8PJB5 View 3D Structure Click here
A0A1D8PRM0 View 3D Structure Click here
A0A1D8PTY8 View 3D Structure Click here
A0A1P8B9U3 View 3D Structure Click here
A0A1P8BG25 View 3D Structure Click here
A0A368UGZ4 View 3D Structure Click here
B4F8R5 View 3D Structure Click here
B6SWK9 View 3D Structure Click here
B7ZXD3 View 3D Structure Click here
B8A1R0 View 3D Structure Click here
F4JAB7 View 3D Structure Click here
I1JBG9 View 3D Structure Click here
I1JHB3 View 3D Structure Click here
I1JIN5 View 3D Structure Click here
I1JQR0 View 3D Structure Click here
I1KA12 View 3D Structure Click here
I1KR53 View 3D Structure Click here
I1KUF1 View 3D Structure Click here
I1L4V4 View 3D Structure Click here
I1LA42 View 3D Structure Click here
I1LVZ8 View 3D Structure Click here
I1M7D8 View 3D Structure Click here
I1MAR9 View 3D Structure Click here
I1MB94 View 3D Structure Click here
I1MB94 View 3D Structure Click here
I1MGH2 View 3D Structure Click here
I1ML02 View 3D Structure Click here
I1MW70 View 3D Structure Click here
I1N8A2 View 3D Structure Click here
I1NBB5 View 3D Structure Click here
K7LBF4 View 3D Structure Click here
K7LBP9 View 3D Structure Click here
K7LQP0 View 3D Structure Click here
K7N397 View 3D Structure Click here
K7V329 View 3D Structure Click here
K7WB31 View 3D Structure Click here
L7N6B0 View 3D Structure Click here
O07430 View 3D Structure Click here
P33363 View 3D Structure Click here
P75949 View 3D Structure Click here
Q0IT77 View 3D Structure Click here
Q0JNF8 View 3D Structure Click here
Q10CU4 View 3D Structure Click here
Q10CU9 View 3D Structure Click here
Q10CV2 View 3D Structure Click here
Q23892 View 3D Structure Click here
Q2QZ84 View 3D Structure Click here
Q53MQ1 View 3D Structure Click here
Q60EH3 View 3D Structure Click here
Q6VB92 View 3D Structure Click here
Q6Z8I7 View 3D Structure Click here
Q6ZG89 View 3D Structure Click here
Q7X6F6 View 3D Structure Click here
Q7X7M4 View 3D Structure Click here
Q8RWM4 View 3D Structure Click here
Q94ED2 View 3D Structure Click here
Q94KD8 View 3D Structure Click here
Q9FGY1 View 3D Structure Click here
Q9FLG1 View 3D Structure Click here
Q9LJN4 View 3D Structure Click here
Q9LXA8 View 3D Structure Click here
Q9LXD6 View 3D Structure Click here
Q9LZJ4 View 3D Structure Click here
Q9P6J6 View 3D Structure Click here
Q9SD68 View 3D Structure Click here
Q9SD72 View 3D Structure Click here
Q9SD73 View 3D Structure Click here
Q9SGZ5 View 3D Structure Click here