Summary: Raffinose synthase or seed imbibition protein Sip1
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This is the Wikipedia entry entitled "Glycoside hydrolase family 36". More...
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Glycoside hydrolase family 36 Edit Wikipedia article
crystal structure of rice alpha-galactosidase
|SCOPe||1ktc / SUPFAM|
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. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Glycoside hydrolase family 36 together with family 31 and family 27 alpha-galactosidases form the glycosyl hydrolase clan GH-D, a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology.
Alpha-galactosidase (EC 188.8.131.52) (melibiase) catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. Escherichia coli alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an Escherichia coli plasmid encoded alpha-galactosidase (gene rafA ) contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase (EC 184.108.40.206) catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.
This family also includes raffinose synthase proteins, also known as seed inhibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase EC 220.127.116.11 is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway.
Glycoside hydrolase family 36 can be subdivided into 11 families, GH36A to GH36K.
- 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): 7090â€“7094. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.
- Henrissat B, Davies G (1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853â€“859. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
- Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
- "Home". CAZy.org. Retrieved 2018-03-06.
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie; Coutinho, Pedro M.; Henrissat, Bernard (2014-01-01). "The carbohydrate-active enzymes database (CAZy) in 2013". Nucleic Acids Research. 42 (D1): D490â€“D495. doi:10.1093/nar/gkt1178. ISSN 0305-1048. PMC 3965031. PMID 24270786.
- "Glycoside Hydrolase Family 36". CAZypedia.org. Retrieved 2018-03-06.
- CAZypedia Consortium (2018-12-01). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes" (PDF). Glycobiology. 28 (1): 3â€“8. doi:10.1093/glycob/cwx089. ISSN 1460-2423. PMID 29040563.
- Dey PM, Pridham JB (1972). "Biochemistry of -galactosidases". Adv. Enzymol. Relat. Areas Mol. Biol. 36: 91â€“120. doi:10.1002/9780470122815.ch3. PMID 4561015.
- Aslanidis C, Schmid K, Schmitt R (1989). "Nucleotide sequences and operon structure of plasmid-borne genes mediating uptake and utilization of raffinose in Escherichia coli". J. Bacteriol. 171 (12): 6753â€“6763. doi:10.1128/jb.171.12.6753-6763.1989. PMC 210573. PMID 2556373.
- Wang AM, Bishop DF, Desnick RJ (1990). "Human alpha-N-acetylgalactosaminidase-molecular cloning, nucleotide sequence, and expression of a full-length cDNA. Homology with human alpha-galactosidase A suggests evolution from a common ancestral gene". J. Biol. Chem. 265 (35): 21859â€“21866. PMID 2174888.
- Peterbauer T, Mach L, Mucha J, Richter A (September 2002). "Functional expression of a cDNA encoding pea (Pisum sativum L.) raffinose synthase, partial purification of the enzyme from maturing seeds, and steady-state kinetic analysis of raffinose synthesis". Planta. 215 (5): 839â€“46. doi:10.1007/s00425-002-0804-7. PMID 12244450.
- Naumoff DG (2011). "Hierarchical classification of glycoside hydrolases". Biochemistry (Moscow). 76 (6): 622â€“35. doi:10.1134/S0006297911060022. PMID 21639842.
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Raffinose synthase or seed imbibition protein Sip1 Provide feedback
This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase ( EC:18.104.22.168) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway . Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions . Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K . This family includes enzymes from GH36C.
Peterbauer T, Mach L, Mucha J, Richter A; , Planta 2002;215:839-846.: Functional expression of a cDNA encoding pea (Pisum sativum L.) raffinose synthase, partial purification of the enzyme from maturing seeds, and steady-state kinetic analysis of raffinose synthesis. PUBMED:12244450 EPMC:12244450
Internal database links
|SCOOP:||Glyco_hydro_31 Melibiase Melibiase_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008811
This family consists of several galactinol-sucrose galactosyltransferase proteins, also known as raffinose synthases, which is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase ( EC ) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway [ PUBMED:12244450 ]. Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions [ PUBMED:18335235 ]. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K [ PUBMED:21639842 ]. This family includes enzymes from GH36C.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This large superfamily contains a range of glycosyl hydrolase enzymes that possess a TIM barrel fold. This CLAN merges clans GH-A, GH-D, GH-H and GH-K from CAZy.
The clan contains the following 59 members:Alpha-amylase Alpha_L_fucos Cellulase Cellulase-like Dehydratase_LU DUF1906 DUF4015 DUF4038 DUF4434 DUF4838 DUF4849 DUF5010 DUF5696 DUF6259 GHL10 GHL13 GHL15 GHL5 GHL6 Glyco_hydr_30_2 Glyco_hydro_1 Glyco_hydro_10 Glyco_hydro_101 Glyco_hydro_114 Glyco_hydro_129 Glyco_hydro_14 Glyco_hydro_17 Glyco_hydro_18 Glyco_hydro_20 Glyco_hydro_25 Glyco_hydro_26 Glyco_hydro_2_C Glyco_hydro_3 Glyco_hydro_30 Glyco_hydro_31 Glyco_hydro_35 Glyco_hydro_39 Glyco_hydro_42 Glyco_hydro_44 Glyco_hydro_53 Glyco_hydro_56 Glyco_hydro_59 Glyco_hydro_66 Glyco_hydro_70 Glyco_hydro_71 Glyco_hydro_72 Glyco_hydro_77 Glyco_hydro_79n Glyco_hydro_85 Glyco_hydro_97 Glyco_hydro_99 Glyco_hydro_cc Glyco_tran_WbsX hDGE_amylase Melibiase Melibiase_2 NAGidase NAGLU Raffinose_syn
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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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.
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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.
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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.
|Seed source:||Pfam-B_3204 (release 8.0)|
|Author:||Moxon SJ , Eberhardt R|
|Number in seed:||4|
|Number in full:||3128|
|Average length of the domain:||433.70 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||76.32 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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.
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.
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