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33  structures 1463  species 0  interactions 2959  sequences 5  architectures

Family: Glyco_hydro_4C (PF11975)

Summary: Family 4 glycosyl hydrolase C-terminal domain

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This is the Wikipedia entry entitled "Glycoside hydrolase family 4". More...

Glycoside hydrolase family 4 Edit Wikipedia article

Family 4 glycosyl hydrolase
PDB 1up6 EBI.jpg
structure of the 6-phospho-beta glucosidase from thermotoga maritima at 2.55 angstrom resolution in the tetragonal form with manganese, nad+ and glucose-6-phosphate
Identifiers
Symbol Glyco_hydro_4
Pfam PF02056
Pfam clan CL0063
InterPro IPR001088
PROSITE PDOC01027
SCOP 1obb
SUPERFAMILY 1obb
CAZy GH4
Family 4 glycosyl hydrolase C-terminal domain
Identifiers
Symbol Glyco_hydro_4C
Pfam PF11975
Pfam clan CL0341
PROSITE PDOC01027
SCOP 1obb
SUPERFAMILY 1obb
CAZy GH4

In molecular biology, glycoside hydrolase family 4 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 4 CAZY GH_4 comprises enzymes with several known activities; 6-phospho-beta-glucosidase (EC 3.2.1.86); 6-phospho-alpha-glucosidase (EC 3.2.1.122); alpha-galactosidase (EC 3.2.1.22). 6-phospho-alpha-glucosidase requires both NAD(H) and divalent metal (Mn2+, Fe2+, Co2+, or Ni2+) for activity.[6]

[edit] External references

GH4 in CAZypedia

[edit] 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. ^ Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
  5. ^ CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
  6. ^ Henrissat B, Thompson J, Yamamoto H, Pikis A, Ruvinov SB, Sekiguchi J (1998). "The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-alpha-glucosidase. Assignment to family 4 of the glycosylhydrolase superfamily". J. Biol. Chem. 273 (42): 27347–27356. doi:10.1074/jbc.273.42.27347. PMID 9765262. 

This article incorporates text from the public domain Pfam and InterPro IPR001088

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.

Family 4 glycosyl hydrolase C-terminal domain Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022616

This domain is found primarily in bacterial family 4 glycosyl hydrolases. It is found in the C terminus.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 LDH_C (CL0341), which has the following description:

This superfamily includes the C-terminal domain of lactate/malate dehydrogenase as well as the C-terminal domain of the glycosyl hydrolase 4 family.

The clan contains the following 2 members:

Glyco_hydro_4C Ldh_1_C

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(8)
Full
(2959)
Representative proteomes NCBI
(1786)
Meta
(410)
RP15
(162)
RP35
(297)
RP55
(368)
RP75
(464)
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Format an alignment

  Seed
(8)
Full
(2959)
Representative proteomes NCBI
(1786)
Meta
(410)
RP15
(162)
RP35
(297)
RP55
(368)
RP75
(464)
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
(8)
Full
(2959)
Representative proteomes NCBI
(1786)
Meta
(410)
RP15
(162)
RP35
(297)
RP55
(368)
RP75
(464)
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:

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: IPR001088
Previous IDs: none
Type: Domain
Author: Mian N, Bateman A
Number in seed: 8
Number in full: 2959
Average length of the domain: 216.50 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 50.24 %

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 21.9 21.9
Trusted cut-off 22.8 21.9
Noise cut-off 20.9 21.6
Model length: 232
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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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_4C domain has been found. There are 33 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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