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0  structures 210  species 0  interactions 570  sequences 15  architectures

Family: Raffinose_syn (PF05691)

Summary: Raffinose synthase or seed imbibition protein Sip1

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This is the Wikipedia entry entitled "Glycoside hydrolase family 36". More...

Glycoside hydrolase family 36 Edit Wikipedia article

Melibiase
PDB 1uas EBI.jpg
crystal structure of rice alpha-galactosidase
Identifiers
Symbol Melibiase
Pfam PF02065
Pfam clan CL0058
InterPro IPR000111
SCOP 1ktc
SUPERFAMILY 1ktc
CAZy GH36
Raffinose_syn
Identifiers
Symbol Raffinose_syn
Pfam PF05691
Pfam clan CL0058
InterPro IPR008811
CAZy GH36

In molecular biology, glycoside hydrolase family 36 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 36 together with family 31 and family 27 alpha-galactosidases form the glycosyl hydrolase clan GH-D (CAZY GH), 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 3.2.1.22) (melibiase)[6] 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 P16551)[7] contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase (EC 3.2.1.49)[8] 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 2.4.1.82 is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway.[9]

Glycoside hydrolase family 36 also includes enzymes with α-N-acetylgalactosaminidase EC 3.2.1.49 and stachyose synthase EC 2.4.1.67 activities.

Glycoside hydrolase family 36 can be subdivided into 11 families, GH36A to GH36K.[10]

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. ^ Dey PM, Pridham JB (1972). "Biochemistry of -galactosidases". Adv. Enzymol. Relat. Areas Mol. Biol. 36: 91–120. PMID 4561015. 
  7. ^ 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): 6753–6763. PMC 210573. PMID 2556373. 
  8. ^ 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): 21859–21866. PMID 2174888. 
  9. ^ 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): 839–46. doi:10.1007/s00425-002-0804-7. PMID 12244450. 
  10. ^ Naumoff DG (2011). "Hierarchical classification of glycoside hydrolases.". Biochemistry (Mosc) 76 (6): 622–35. doi:10.1134/S0006297911060022. PMID 21639842. 

This article incorporates text from the public domain Pfam and InterPro IPR000111

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.

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:2.4.1.82) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway [1]. 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 [2]. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K [3]. This family includes enzymes from GH36C.

Literature references

  1. 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

  2. Blochl A, Peterbauer T, Hofmann J, Richter A;, Planta. 2008;228:99-110.: Enzymatic breakdown of raffinose oligosaccharides in pea seeds. PUBMED:18335235 EPMC:18335235

  3. Naumoff DG;, Biochemistry (Mosc). 2011;76:622-635.: Hierarchical classification of glycoside hydrolases. PUBMED:21639842 EPMC:21639842


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008811

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) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway [PUBMED:12244450].

Domain organisation

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(11)
Full
(570)
Representative proteomes NCBI
(620)
Meta
(6)
RP15
(71)
RP35
(176)
RP55
(235)
RP75
(281)
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  Seed
(11)
Full
(570)
Representative proteomes NCBI
(620)
Meta
(6)
RP15
(71)
RP35
(176)
RP55
(235)
RP75
(281)
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  Seed
(11)
Full
(570)
Representative proteomes NCBI
(620)
Meta
(6)
RP15
(71)
RP35
(176)
RP55
(235)
RP75
(281)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Curation and family details

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Seed source: Pfam-B_3204 (release 8.0)
Previous IDs: none
Type: Family
Author: Moxon SJ, Eberhardt R
Number in seed: 11
Number in full: 570
Average length of the domain: 368.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 73.23 %

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 20.0 20.0
Trusted cut-off 20.1 20.1
Noise cut-off 19.8 19.8
Model length: 747
Family (HMM) version: 7
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