Summary: Glycosyl hydrolase family 67 N-terminus
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Glycoside hydrolase family 67 Edit Wikipedia article
| Glycosyl hydrolase family 67 N-terminus | |||||||||
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 the 1.7 a crystal structure of alpha-d-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus t-1 | |||||||||
| Identifiers | |||||||||
| Symbol | Glyco_hydro_67N | ||||||||
| Pfam | PF03648 | ||||||||
| InterPro | IPR005154 | ||||||||
| SCOPe | 1h41 / SUPFAM | ||||||||
| CAZy | GH67 | ||||||||
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| Glycosyl hydrolase family 67 middle domain | |||||||||
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 pseudomonas cellulosa e292a alpha-d-glucuronidase mutant complexed with aldotriuronic acid | |||||||||
| Identifiers | |||||||||
| Symbol | Glyco_hydro_67M | ||||||||
| Pfam | PF07488 | ||||||||
| InterPro | IPR011100 | ||||||||
| SCOPe | 1h41 / SUPFAM | ||||||||
| CAZy | GH67 | ||||||||
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| Glycosyl hydrolase family 67 C-terminus | |||||||||
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the 1.7 a crystal structure of alpha-d-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus t-1 | |||||||||
| Identifiers | |||||||||
| Symbol | Glyco_hydro_67C | ||||||||
| Pfam | PF07477 | ||||||||
| InterPro | IPR011099 | ||||||||
| SCOPe | 1h41 / SUPFAM | ||||||||
| CAZy | GH67 | ||||||||
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In molecular biology, glycoside hydrolase family 67 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]
Glycoside hydrolase family 67 includes alpha-glucuronidases, these are components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans.
Members of this family consist of three structural domains. Deletion mutants of alpha-glucuronidase from Bacillus stearothermophilus have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus) are thought to form the catalytic centre.[8] The C-terminal region of alpha-glucuronidase is mainly alpha-helical. It wraps around the catalytic domain, making additional interactions both with the N-terminal domain of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer.[9]
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) (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 67". 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. hdl:21.11116/0000-0003-B7EB-6. PMID 29040563.
- ^ Shoham Y, Zaide G, Shallom D, Shulami S, Zolotnitsky G, Golan G, Baasov T, Shoham G (2001). "Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6". Eur. J. Biochem. 268 (10): 3006–3016. doi:10.1046/j.1432-1327.2001.02193.x. PMID 11358519.
- ^ Nurizzo D, Nagy T, Gilbert HJ, Davies GJ (April 2002). "The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A". Structure. 10 (4): 547–56. doi:10.1016/s0969-2126(02)00742-6. PMID 11937059.
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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 hydrolase family 67 N-terminus Provide feedback
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices form part of the interface with the central, catalytic, module (PF07488) [1].
Literature references
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Nurizzo D, Nagy T, Gilbert HJ, Davies GJ; , Structure (Camb) 2002;10:547-556.: The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. PUBMED:11937059 EPMC:11937059
Internal database links
| SCOOP: | Glyco_hydro_20b |
| Similarity to PfamA using HHSearch: | Glyco_hydro_20b |
External database links
| CAZY: | GH67 |
| SCOP: | 1h41 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005154
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 represents a family of alpha-glucuronidases (CAZY). Deletion mutants have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus (Geobacillus stearothermophilus)) are thought to from the the catalytic centre [PUBMED:11358519].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | alpha-glucuronidase activity (GO:0046559) |
| Biological process | xylan catabolic process (GO:0045493) |
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 Hexosaminidase (CL0546), which has the following description:
This superfamily is characterised by a mixed beta sheet with connection over the free side of the sheet. The fold is like a zincin fold lacking the catalytic centre.
The clan contains the following 5 members:
GcnA_N Glyco_hydro_20b Glyco_hydro_67N Glycohydro_20b2 NAGLU_NAlignments
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...
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| Seed (23) |
Full (960) |
Representative proteomes | UniProt (3179) |
NCBI (4592) |
Meta (17) |
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| RP15 (83) |
RP35 (369) |
RP55 (816) |
RP75 (1511) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (23) |
Full (960) |
Representative proteomes | UniProt (3179) |
NCBI (4592) |
Meta (17) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (83) |
RP35 (369) |
RP55 (816) |
RP75 (1511) |
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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: | CAZY |
| Previous IDs: | Glyco_hydro_67; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Moxon SJ
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| Number in seed: | 23 |
| Number in full: | 960 |
| Average length of the domain: | 115.20 aa |
| Average identity of full alignment: | 24 % |
| Average coverage of the sequence by the domain: | 14.93 % |
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: | 121 | ||||||||||||
| Family (HMM) version: | 15 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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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_67N domain has been found. There are 17 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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