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24  structures 990  species 5  interactions 2134  sequences 61  architectures

Family: GH97_N (PF14508)

Summary: Glycosyl-hydrolase 97 N-terminal

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This is the Wikipedia entry entitled "Glycoside hydrolase family 97". More...

Glycoside hydrolase family 97 Edit Wikipedia article

Glycoside hydrolase 97
Identifiers
SymbolGlyco_hydro_97
PfamPF10566
Pfam clanCL0058
InterProIPR019563

In molecular biology, glycoside hydrolase family 97 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 97 (GH97) is a bacterial family. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands.[8]

External links

References

  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. ^ "Home". CAZy.org. Retrieved 2018-03-06.
  5. ^ 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): D490–D495. doi:10.1093/nar/gkt1178. ISSN 0305-1048. PMC 3965031. PMID 24270786.
  6. ^ "Glycoside Hydrolase Family 97". CAZypedia.org. Retrieved 2018-03-06.
  7. ^ CAZypedia Consortium (2018-12-01). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes". Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. hdl:21.11116/0000-0003-B7EB-6. ISSN 1460-2423. PMID 29040563.
  8. ^ Naumoff DG (2005). "GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily". BMC Genomics. 6: 112. doi:10.1186/1471-2164-6-112. PMC 1249566. PMID 16131397.
This article incorporates text from the public domain Pfam and InterPro: IPR019563

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-hydrolase 97 N-terminal Provide feedback

This N-terminal domain of glycosyl-hydrolase-97 [1] part of the active site pocket. It is also important for contact with the catalytic and C-terminal domains of the whole [2,3].

Literature references

  1. Naumoff DG; , BMC Genomics. 2005;6:112.: GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. PUBMED:16131397 EPMC:16131397

  2. Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ;, Chem Biol. 2008;15:1058-1067.: Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. PUBMED:18848471 EPMC:18848471

  3. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M;, J Biol Chem. 2008;283:36328-36337.: Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. PUBMED:18981178 EPMC:18981178


This tab holds annotation information from the InterPro database.

InterPro entry IPR029486

Proteins containing this domain include the aglycoside hydrolase family 97 enzyme, SusB protein, from Bacteroides thetaiotaomicron. SusB has three domains: the N-terminal, catalytic, and C-terminal domains. This entry represents the N-terminal domain that contributes to part of the active site pocket and is important for contact with the catalytic and the C-terminal domains [PUBMED:18848471, PUBMED:18981178].

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 Gal_mutarotase (CL0103), which has the following description:

This clan is composed of a beta-sandwich that was first observed in domain 5 of beta-galactosidase, then as the central domain of copper amine oxidase, the C-terminal domain of chondroitinase, the C-terminal domain of hyaluronate lyase, the N-terminal domain of maltose phosphorylase and in Galactose Mutarotase [1]. All these enzymes act on a sugar substrate.

The clan contains the following 32 members:

Aldose_epim Bgal_small_N Cu_amine_oxid DUF1926 DUF4432 DUF4450 DUF4968 DUF5054 DUF5107 DUF5127 DUF5703_N Gal_mutarotas_2 Gal_mutarotas_3 GH97_N Glucodextran_N Glyco_hyd_65N_2 Glyco_hydr_116N Glyco_hydro_36N Glyco_hydro_38 Glyco_hydro_38C Glyco_hydro_52 Glyco_hydro_65N Glyco_hydro_81 Glyco_hydro_92N Glyco_transf_36 Hepar_II_III Lyase_8 MdoG NtCtMGAM_N Rhamnogal_lyase RhgB_N YidC_periplas

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 (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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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
(258)
Full
(2134)
Representative proteomes UniProt
(9634)
NCBI
(13292)
Meta
(147)
RP15
(152)
RP35
(809)
RP55
(2174)
RP75
(4504)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(258)
Full
(2134)
Representative proteomes UniProt
(9634)
NCBI
(13292)
Meta
(147)
RP15
(152)
RP35
(809)
RP55
(2174)
RP75
(4504)
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
(258)
Full
(2134)
Representative proteomes UniProt
(9634)
NCBI
(13292)
Meta
(147)
RP15
(152)
RP35
(809)
RP55
(2174)
RP75
(4504)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: PF10566-seed
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 258
Number in full: 2134
Average length of the domain: 256.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 37.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.3 25.3
Trusted cut-off 27.0 26.7
Noise cut-off 22.4 25.1
Model length: 233
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 5 interactions for this family. More...

Glyco_hydro_97 GH97_C GH97_N Glyco_hydro_97 GH97_C

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 GH97_N domain has been found. There are 24 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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