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658  structures 1340  species 3  interactions 3255  sequences 30  architectures

Family: Phage_lysozyme (PF00959)

Summary: Phage lysozyme

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This is the Wikipedia entry entitled "Glycoside hydrolase family 24". More...

Glycoside hydrolase family 24 Edit Wikipedia article

Phage lysozyme
PDB 1am7 EBI.jpg
lysozyme from bacteriophage lambda
Identifiers
Symbol Phage_lysozyme
Pfam PF00959
Pfam clan CL0037
InterPro IPR002196
SCOP 119l
SUPERFAMILY 119l
CAZy GH24

In molecular biology, glycoside hydrolase family 24 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 24 CAZY GH_24 comprises enzymes with only one known activity; lysozyme (EC 3.2.1.17). This family includes lambda phage lysozyme and Escherichia coli endolysin.[6] Lysozyme helps to release mature phage particles from the cell wall by breaking down the peptidoglycan. The enzyme hydrolyses the 1,4-beta linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of prokaryotic cell walls. E. coli endolysin also functions in bacterial cell lysis and acts as a transglycosylase. The T4 lysozyme structure contains 2 domains, the interface between which forms the active-site cleft. The N-terminus of the 2 domains undergoes a 'hinge-bending' motion about an axis passing through the molecular waist.[6][7] This mobility is thought to be important in allowing access of substrates to the enzyme active site.

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 Matthews BW, Weaver LH (1987). "Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution". J. Mol. Biol. 193 (1): 189–199. doi:10.1016/0022-2836(87)90636-X. PMID 3586019. 
  7. ^ Matthews BW, Faber HR (1990). "A mutant T4 lysozyme displays five different crystal conformations". Nature 348 (6298): 263–266. doi:10.1038/348263a0. PMID 2234094. 

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.

Phage lysozyme Provide feedback

This family includes lambda phage lysozyme and E. coli endolysin.

Literature references

  1. Weaver LH, Matthews BW; , J Mol Biol 1987;193:189-199.: Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution. PUBMED:3586019 EPMC:3586019


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002196

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.

Glycoside hydrolase family 24 CAZY comprises enzymes with only one known activity; lysozyme (EC).

This entry includes Bacteriophage lambda lysozyme and Escherichia coli endolysin [PUBMED:3586019]. Lysozyme helps to release mature phage particles from the cell wall by breaking down the peptidoglycan. The enzyme hydrolyses the 1,4-beta linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of prokaryotic cell walls. E. coli endolysin also functions in bacterial cell lysis and acts as a transglycosylase. The Bacteriophage T4 lysozyme structure contains 2 domains, the interface between which forms the active-site cleft. The N terminus of the 2 domains undergoes a 'hinge-bending' motion about an axis passing through the molecular waist [PUBMED:3586019, PUBMED:2234094]. This mobility is thought to be important in allowing access of substrates to the enzyme active site.

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 Lysozyme (CL0037), which contains the following 12 members:

Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Lys Lysozyme_like Phage_lysozyme REGB_T4 SLT SLT_2 TraH_2 Transglycosylas

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
(18)
Full
(3255)
Representative proteomes NCBI
(2608)
Meta
(736)
RP15
(74)
RP35
(208)
RP55
(308)
RP75
(411)
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Format an alignment

  Seed
(18)
Full
(3255)
Representative proteomes NCBI
(2608)
Meta
(736)
RP15
(74)
RP35
(208)
RP55
(308)
RP75
(411)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(18)
Full
(3255)
Representative proteomes NCBI
(2608)
Meta
(736)
RP15
(74)
RP35
(208)
RP55
(308)
RP75
(411)
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: Sarah Teichmann
Previous IDs: none
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 18
Number in full: 3255
Average length of the domain: 110.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 59.84 %

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 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 110
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Gp5_C Gp5_OB Phage_lysozyme

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 Phage_lysozyme domain has been found. There are 658 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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