Summary: Beta-galactosidase trimerisation domain
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This is the Wikipedia entry entitled "Glycoside hydrolase family 42". More...
Glycoside hydrolase family 42 Edit Wikipedia article
Beta-galactosidase | |||||||||
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![]() crystal structure of thermus thermophilus a4 beta-galactosidase | |||||||||
Identifiers | |||||||||
Symbol | Glyco_hydro_42 | ||||||||
Pfam | PF02449 | ||||||||
Pfam clan | CL0058 | ||||||||
InterPro | IPR013529 | ||||||||
SCOPe | 1kwg / SUPFAM | ||||||||
CAZy | GH42 | ||||||||
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Beta-galactosidase trimerisation domain | |||||||||
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![]() crystal structure of thermus thermophilus a4 beta-galactosidase | |||||||||
Identifiers | |||||||||
Symbol | Glyco_hydro_42M | ||||||||
Pfam | PF08532 | ||||||||
Pfam clan | CL0014 | ||||||||
InterPro | IPR013738 | ||||||||
SCOPe | 1kwg / SUPFAM | ||||||||
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Beta-galactosidase C-terminal domain | |||||||||
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![]() crystal structure of thermus thermophilus a4 beta-galactosidase | |||||||||
Identifiers | |||||||||
Symbol | Glyco_hydro_42C | ||||||||
Pfam | PF08533 | ||||||||
Pfam clan | CL0369 | ||||||||
InterPro | IPR013739 | ||||||||
SCOPe | 1kwg / SUPFAM | ||||||||
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In molecular biology, glycoside hydrolase family 42 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]
The glycosyl hydrolase 42 family CAZY GH_42 comprises beta-galactosidase enzymes (EC 3.2.1.23). These enzyme catalyse the hydrolysis of terminal, non-reducing terminal beta-D-galactoside residues. The middle domain of these three-domain enzymes is involved in trimerisation.[8]
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ "Home". CAZy.org. Retrieved 2018-03-06.
- ^ 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.
- ^ "Glycoside Hydrolase Family 42". CAZypedia.org. Retrieved 2018-03-06.
- ^ 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.
- ^ Shimizu T, Kobayashi T, Ba-Thein W, Ohtani K, Hayashi H (1995). "Sequence analysis of flanking regions of the pfoA gene of Clostridium perfringens: beta-galactosidase gene (pbg) is located in the 3'-flanking region". Microbiology and Immunology. 39 (9): 677–86. doi:10.1111/j.1348-0421.1995.tb03256.x. PMID 8577281.
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.
Beta-galactosidase trimerisation domain Provide feedback
This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation [1].
Literature references
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Shimizu T, Kobayashi T, Ba-Thein W, Ohtani K, Hayashi H; , Microbiol Immunol 1995;39:677-686.: Sequence analysis of flanking regions of the pfoA gene of Clostridium perfringens: beta-galactosidase gene (pbg) is located in the 3'-flanking region. PUBMED:8577281 EPMC:8577281
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Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T; , J Mol Biol 2002;322:79-91.: Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. PUBMED:12215416 EPMC:12215416
Internal database links
SCOOP: | LBP_M ThuA |
Similarity to PfamA using HHSearch: | LBP_M |
External database links
SCOP: | 1kwg |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013738
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.
This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | beta-galactosidase activity (GO:0004565) |
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 Glutaminase_I (CL0014), which has the following description:
Most members of this clan are glutaminase enzymes. This superfamily is shown to be related in [1]. The clan also contains the DJ-1/PfpI family that includes the peptidase PfpI that has a catalytic Cys-His-Glu triad that differs from the class I GAT Cys-His-Glu triad.
The clan contains the following 18 members:
ABC_transp_aux BPL_N Catalase_C DJ-1_PfpI DUF4159 GATase GATase1_like GATase_3 GATase_5 Glyco_hydro_42M HTS LBP_M Peptidase_C26 Peptidase_S51 Peptidase_S66 SNO ThiJ_like ThuAAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (18) |
Full (3331) |
Representative proteomes | UniProt (13046) |
NCBI (21646) |
Meta (152) |
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RP15 (243) |
RP35 (1445) |
RP55 (3457) |
RP75 (6030) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an 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 (18) |
Full (3331) |
Representative proteomes | UniProt (13046) |
NCBI (21646) |
Meta (152) |
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RP15 (243) |
RP35 (1445) |
RP55 (3457) |
RP75 (6030) |
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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: | Pfam-B_2131 (release 5.4) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 18 |
Number in full: | 3331 |
Average length of the domain: | 195.60 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 29.36 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 207 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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Interactions
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_42M domain has been found. There are 31 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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