Summary: Glycosyl hydrolases family 28
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This is the Wikipedia entry entitled "Glycoside hydrolase family 28". More...
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Glycosyl hydrolases family 28 Provide feedback
Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolism.
Literature references
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Petersen TN, Kauppinen S, Larsen S; , Structure 1997;5:533-544.: The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix. PUBMED:9115442 EPMC:9115442
Internal database links
SCOOP: | Beta_helix DUF1565 NosD Pectate_lyase_3 Pectate_lyase_4 |
Similarity to PfamA using HHSearch: | Beta_helix |
External database links
CAZY: | GH28 |
HOMSTRAD: | ghf28 |
PROSITE: | PDOC00415 |
SCOP: | 1rmg |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000743
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 28 CAZY comprises enzymes with several known activities; polygalacturonase ( EC ); exo-polygalacturonase ( EC ); exo-polygalacturonase ( EC ); rhamnogalacturonase (EC not defined).
Polygalacturonase (PG) (pectinase) [ PUBMED:2400785 , PUBMED:2193922 ] catalyses the random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans. In fruit, polygalacturonase plays an important role in cell wall metabolism during ripening. In plant bacterial pathogens such as Erwinia carotovora or Ralstonia solanacearum (Pseudomonas solanacearum) and fungal pathogens such as Aspergillus niger, polygalacturonase is involved in maceration and soft-rotting of plant tissue. Exo-poly-alpha-D-galacturonosidase ( EC ) (exoPG) [ PUBMED:2168372 ] hydrolyses peptic acid from the non-reducing end, releasing digalacturonate. PG and exoPG share a few regions of sequence similarity, and belong to family 28 of the glycosyl hydrolases.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | polygalacturonase activity (GO:0004650) |
Biological process | carbohydrate metabolic process (GO:0005975) |
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 Pec_lyase-like (CL0268), which has the following description:
This superfamily all contain a right handed beta helix similar to that first found in pectate lyase [1].
The clan contains the following 39 members:
AC_1 Adeno_E1B_55K AIDA B_solenoid_dext B_solenoid_ydck Bactofilin Beta_helix Beta_helix_2 Beta_helix_3 Chlam_PMP Chondroitinas_B Cthe_2159 Disaggr_assoc DUF1565 DUF2154 DUF2807 DUF3737 DUF4097 DUF4957 DUF5649 End_N_terminal FapA Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_92 Haemagg_act IPU_b_solenoid NosD PATR Pectate_lyase Pectate_lyase_3 Pectate_lyase_4 Pectinesterase Pertactin PhageP22-tail Toast_rack_N VacAAlignments
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 (11) |
Full (18488) |
Representative proteomes | UniProt (39490) |
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RP15 (1717) |
RP35 (8839) |
RP55 (15124) |
RP75 (22745) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (11) |
Full (18488) |
Representative proteomes | UniProt (39490) |
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RP15 (1717) |
RP35 (8839) |
RP55 (15124) |
RP75 (22745) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | PG; |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Finn RD |
Number in seed: | 11 |
Number in full: | 18488 |
Average length of the domain: | 281.60 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 68.43 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 325 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
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_28 domain has been found. There are 39 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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