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177  structures 627  species 7  interactions 1575  sequences 87  architectures

Family: Glyco_hydro_11 (PF00457)

Summary: Glycosyl hydrolases family 11

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This is the Wikipedia entry entitled "Glycoside hydrolase family 11". More...

Glycoside hydrolase family 11 Edit Wikipedia article

Glycosyl hydrolases family 11
PDB 1m4w EBI.jpg
thermophilic b-1,4-xylanase from nonomuraea flexuosa
Identifiers
Symbol Glyco_hydro_11
Pfam PF00457
Pfam clan CL0004
InterPro IPR001137
PROSITE PDOC00622
SCOP 1xnd
SUPERFAMILY 1xnd
CAZy GH11

In molecular biology, Glycoside hydrolase family 11 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 11 CAZY GH_11 comprises enzymes with only one known activity, xylanase (EC 3.2.1.8). These enzymes were formerly known as cellulase family G.

References

  1. ^ 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 41477Freely accessible. PMID 7624375. 
  2. ^ 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. 
  3. ^ Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 ( Pt 2) (Pt 2): 695–6. PMC 1217404Freely accessible. PMID 8687420. 
  4. ^ "Home". CAZy.org. Retrieved 2018-03-06. 
  5. ^ 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. PMID 24270786. 
  6. ^ "Glycoside Hydrolase Family 11". CAZypedia.org. Retrieved 2018-03-06. 
  7. ^ "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes". Glycobiology. 28 (1): 3–8. December 2018. doi:10.1093/glycob/cwx089. PMID 29040563. 

This article incorporates text from the public domain Pfam and InterPro IPR001137

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR033123

The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (EC), cellobiohydrolases (EC) (exoglucanases), or xylanases (EC) [PUBMED:2252383, PUBMED:1886523]. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family G [PUBMED:2806912] or as the glycosyl hydrolases family 11 (GH11) [PUBMED:1747104].

The GH11 domain folds into a jelly-roll shape likened to a partially closed right hand. Several anti-parallel beta-strands bend almost 90deg to produce a substrate-binding groove characteristic of the GH11 domain active sites. Two catalytic Glu residues face each other from opposite sides of the groove. The hydrolysis reaction is believed to follow a double- displacement mechanism, with one Glu residue acting as a general acid/base catalyst and the other as a nucleophile.

Domain organisation

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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
(174)
Full
(1575)
Representative proteomes UniProt
(3257)
NCBI
(3981)
Meta
(0)
RP15
(269)
RP35
(880)
RP55
(1352)
RP75
(1804)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(174)
Full
(1575)
Representative proteomes UniProt
(3257)
NCBI
(3981)
Meta
(0)
RP15
(269)
RP35
(880)
RP55
(1352)
RP75
(1804)
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
(174)
Full
(1575)
Representative proteomes UniProt
(3257)
NCBI
(3981)
Meta
(0)
RP15
(269)
RP35
(880)
RP55
(1352)
RP75
(1804)
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.

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: Prosite
Previous IDs: glycosyl_hydro6;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 174
Number in full: 1575
Average length of the domain: 177.30 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 60.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 22.9 22.6
Noise cut-off 21.3 21.2
Model length: 178
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 7 interactions for this family. More...

TAXi_N Glyco_hydro_11 CBM_6 TAXi_C TAXi_C Glyco_hydro_18 CBM_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_11 domain has been found. There are 177 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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