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34  structures 2112  species 1  interaction 5906  sequences 121  architectures

Family: Glyco_hydro_3_C (PF01915)

Summary: Glycosyl hydrolase family 3 C-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
Symbol Glyco_hydro_3
Pfam PF00933
Pfam clan CL0058
InterPro IPR001764
PROSITE PDOC00621
SCOP 1ex1
SUPERFAMILY 1ex1
CAZy GH3
Glycosyl hydrolase family 3 C-terminal domain
PDB 1ieq EBI.jpg
crystal structure of barley beta-d-glucan glucohydrolase isoenzyme exo1
Identifiers
Symbol Glyco_hydro_3_C
Pfam PF01915
InterPro IPR002772
PROSITE PDOC00621
SCOP 1ex1
SUPERFAMILY 1ex1

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(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 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.[6]

External references[edit]

GH3 in CAZypedia

References[edit]

  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. 
  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. ^ Varghese JN, Fincher GB, Hrmova M (1999). "Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase". Structure 7 (2): 179–190. 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 C-terminal domain Provide feedback

This domain is involved in catalysis and may be involved in binding beta-glucan [1]. This domain is found associated with PF00933.

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002772

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 entry represents the C-terminal domain, involved in catalysis and may be involved in binding beta-glucan [PUBMED:10368285]. It is found associated with .

Gene Ontology

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Domain organisation

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Alignments

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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
(107)
Full
(5906)
Representative proteomes NCBI
(5621)
Meta
(1277)
RP15
(741)
RP35
(1451)
RP55
(1968)
RP75
(2239)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(107)
Full
(5906)
Representative proteomes NCBI
(5621)
Meta
(1277)
RP15
(741)
RP35
(1451)
RP55
(1968)
RP75
(2239)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(107)
Full
(5906)
Representative proteomes NCBI
(5621)
Meta
(1277)
RP15
(741)
RP35
(1451)
RP55
(1968)
RP75
(2239)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Bateman A, Griffiths-Jones SR
Number in seed: 107
Number in full: 5906
Average length of the domain: 251.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 33.08 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.7 21.5
Noise cut-off 21.4 21.4
Model length: 227
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Glyco_hydro_3

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_C domain has been found. There are 34 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 seqence.

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