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44  structures 332  species 1  interaction 628  sequences 33  architectures

Family: Glyco_hydro_6 (PF01341)

Summary: Glycosyl hydrolases family 6

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This is the Wikipedia entry entitled "Glycoside hydrolase family 6". More...

Glycoside hydrolase family 6 Edit Wikipedia article

Glycosyl hydrolases family 6
Identifiers
Symbol Glyco_hydro_6
Pfam PF01341
InterPro IPR001524
SCOP 1cb2
SUPERFAMILY 1cb2
CAZy GH6

In molecular biology, glycoside hydrolase family 6 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 6 CAZY GH_6 comprises enzymes with several known activities including endoglucanase (EC 3.2.1.4) and cellobiohydrolase (EC 3.2.1.91). These enzymes were formerly known as cellulase family B. The 3D structure of the enzymatic core of cellobiohydrolase II (CBHII) from the fungus Trichoderma reesei reveals an alpha-beta protein with a fold similar to the ubiquitous barrel topology first seen in triose phosphate isomerase.[6] The active site of CBHII is located at the C-terminal end of a parallel beta barrel, in an enclosed tunnel through which the cellulose threads. Two aspartic acid residues, located in the centre of the tunnel are the probable catalytic residues.[6]

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. ^ a b Rouvinen J, Jones TA, Bergfors T, Knowles JK, Teeri T (1990). "Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei". Science 249 (4967): 380–386. doi:10.1126/science.2377893. PMID 2377893. 

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Literature references

  1. Koivula A, Reinikainen T, Ruohonen L, Valkeajarvi A, Claeyssens M, Teleman O, Kleywegt GJ, Szardenings M, Rouvinen J, Jones TA, Teeri TT; , Protein Eng 1996;9:691-699.: The active site of Trichoderma reesei cellobiohydrolase II: the role of tyrosine 169. PUBMED:8875646 EPMC:8875646


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016288

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.

The 1,4-beta cellobiohydrolase family plays a central role in the recycling of plant biomass. The biological conversion of cellulose to glucose generally requires three types of hydrolytic enzymes: Endoglucanases, which cut internal beta-1,4-glucosidic bonds; Exocellobiohydrolases that cut the dissaccharide cellobiose from the non-reducing end of the cellulose polymer chain; and Beta-1,4-glucosidases, which hydrolyze the cellobiose and other short cello-oligosaccharides to glucose.

Gene Ontology

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Domain organisation

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Alignments

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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.

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(74)
Full
(628)
Representative proteomes NCBI
(614)
Meta
(35)
RP15
(93)
RP35
(195)
RP55
(260)
RP75
(282)
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  Seed
(74)
Full
(628)
Representative proteomes NCBI
(614)
Meta
(35)
RP15
(93)
RP35
(195)
RP55
(260)
RP75
(282)
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
(74)
Full
(628)
Representative proteomes NCBI
(614)
Meta
(35)
RP15
(93)
RP35
(195)
RP55
(260)
RP75
(282)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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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.

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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.

Curation View help on the curation process

Seed source: Sarah Teichmann
Previous IDs: Glycosyl_hydr21;
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 74
Number in full: 628
Average length of the domain: 289.60 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 63.55 %

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 17.7 17.7
Trusted cut-off 17.7 17.7
Noise cut-off 17.2 16.6
Model length: 298
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Glyco_hydro_6

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_6 domain has been found. There are 44 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 seqence.

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