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30  structures 822  species 2  interactions 3587  sequences 63  architectures

Family: Glyco_hydro_28 (PF00295)

Summary: Glycosyl hydrolases family 28

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This is the Wikipedia entry entitled "Glycoside hydrolase family 28". More...

Glycoside hydrolase family 28 Edit Wikipedia article

Glycosyl hydrolases family 28
PDB 1rmg EBI.jpg
rhamnogalacturonase a from aspergillus aculeatus
Identifiers
Symbol Glyco_hydro_28
Pfam PF00295
Pfam clan CL0268
InterPro IPR000743
PROSITE PDOC00415
SCOP 1rmg
SUPERFAMILY 1rmg
CAZy GH28

In molecular biology, glycoside hydrolase family 28 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 28 CAZY GH_28 comprises enzymes with several known activities; polygalacturonase (EC 3.2.1.15); exo-polygalacturonase (EC 3.2.1.67); exo-polygalacturonase (EC 3.2.1.82); rhamnogalacturonase (EC not defined).

Polygalacturonase (PG) (pectinase)[6][7] catalyzes 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[disambiguation needed] and soft-rotting of plant tissue. Exo-poly-alpha-D-galacturonosidase (EC 3.2.1.82) (exoPG)[8] hydrolyzes 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.

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. ^ Ruttkowski E, Labitzke R, Khanh NQ, Gottschalk M, Jany KD, Loffler F (1990). "Cloning and DNA sequence analysis of a polygalacturonase cDNA from Aspergillus niger RH5344". Biochim. Biophys. Acta 1087 (1): 104–106. PMID 2400785. 
  7. ^ Schell MA, Huang JH (1990). "DNA sequence analysis of pglA and mechanism of export of its polygalacturonase product from Pseudomonas solanacearum". J. Bacteriol. 172 (7): 3879–3887. PMC 213369. PMID 2193922. 
  8. ^ He SY, Collmer A (1990). "Molecular cloning, nucleotide sequence, and marker exchange mutagenesis of the exo-poly-alpha-D-galacturonosidase-encoding pehX gene of Erwinia chrysanthemi EC16". J. Bacteriol. 172 (9): 4988–4995. PMC 213154. PMID 2168372. 

This article incorporates text from the public domain Pfam and InterPro IPR000743

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 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

  1. 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


External database links

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) web site.

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

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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 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 22 members:

Adeno_E1B_55K Autotrns_rpt Beta_helix Chlam_PMP Chondroitinas_B Disaggr_assoc DUF1565 DUF3737 Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_80 Glyco_hydro_92 Haemagg_act NosD Pec_lyase_C Pectate_lyase Pectate_lyase_3 Pectinesterase Pertactin PhageP22-tail

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(16)
Full
(3587)
Representative proteomes NCBI
(3608)
Meta
(74)
RP15
(359)
RP35
(933)
RP55
(1245)
RP75
(1506)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(16)
Full
(3587)
Representative proteomes NCBI
(3608)
Meta
(74)
RP15
(359)
RP35
(933)
RP55
(1245)
RP75
(1506)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(16)
Full
(3587)
Representative proteomes NCBI
(3608)
Meta
(74)
RP15
(359)
RP35
(933)
RP55
(1245)
RP75
(1506)
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.

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: PG;
Type: Domain
Author: Finn RD
Number in seed: 16
Number in full: 3587
Average length of the domain: 283.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 67.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.3 20.2
Noise cut-off 20.1 20.1
Model length: 326
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Glyco_hydro_28 fn3

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 30 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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