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27  structures 6290  species 0  interactions 13527  sequences 410  architectures

Family: Amidase_3 (PF01520)

Summary: N-acetylmuramoyl-L-alanine amidase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "N-acetylmuramoyl-L-alanine amidase". More...

N-acetylmuramoyl-L-alanine amidase Edit Wikipedia article

In enzymology, a N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) is an enzyme that catalyzes a chemical reaction that cleaves the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

This enzyme belongs to the family of hydrolases, specifically those acting on carbon-nitrogen bonds other than peptide bonds in linear amides. The systematic name of this enzyme class is peptidoglycan amidohydrolase. Other names in common use include acetylmuramyl-L-alanine amidase, N-acetylmuramyl-L-alanine amidase, N-acylmuramyl-L-alanine amidase, acetylmuramoyl-alanine amidase, N-acetylmuramic acid L-alanine amidase, acetylmuramyl-alanine amidase, N-acetylmuramylalanine amidase, murein hydrolase, N-acetylmuramoyl-L-alanine amidase type I, and N-acetylmuramoyl-L-alanine amidase type II. This enzyme participates in peptidoglycan biosynthesis.

Structural studies

As of late 2007, 13 structures have been solved for this class of enzymes, with PDB accession codes 1ARO, 1GVM, 1H8G, 1HCX, 1J3G, 1JWQ, 1LBA, 1X60, 1XOV, 2AR3, 2BGX, 2BH7, and 2BML.

References

Template:Enzyme references

  • Campbell JN (1969). "An improved technique for the preparation of Streptomyces peptidases and N-acetylmuramyl-l-alanine amidase active on bacterial wall peptidoglycans". Biochemistry. 8: 213–22. PMID 5777325.
  • Herbold DR, Glaser L (1975). "Interaction of N-acetylmuramic acid L-alanine amidase with cell wall polymers". J. Biol. Chem. 250: 7231–8. PMID 809432.
  • Herbold DR, Glaser L (1975). "Bacillus subtilis N-acetylmuramic acid L-alanine amidase". J. Biol. Chem. 250: 1676–82. PMID 803507.
  • Ward JB, Curtis CA, Taylor C, Buxton RS (1982). "Purification and characterization of two phage PBSX-induced lytic enzymes of Bacillus subtilis 168: an N-acetylmuramoyl-L-alanine amidase and an N-acetylmuramidase". J. Gen. Microbiol. 128: 1171–8. PMID 6126517.{{cite journal}}: CS1 maint: multiple names: authors list (link)

External links

The CAS registry number for this enzyme class is Template:CAS registry.

Template:Enzyme links

Gene Ontology (GO) codes

Template:GO code links

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.

N-acetylmuramoyl-L-alanine amidase Provide feedback

This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.

Literature references

  1. Kuroda A, Sugimoto Y, Funahashi T, Sekiguchi J; , Mol Gen Genet 1992;234:129-137.: Genetic structure, isolation and characterization of a Bacillus licheniformis cell wall hydrolase. PUBMED:1495475 EPMC:1495475


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002508

N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination.

In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division [ PUBMED:16855223 ]. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins [ PUBMED:18266855 ].

The amidase catalytic module is fused to another functional module (cell wall binding module) either at the N or C terminus, which is responsible for high affinity binding of the protein to the cell wall [ PUBMED:23927005 ].

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 Peptidase_MH (CL0035), which has the following description:

This clan contains peptidases belonging to MEROPS clan MH, MC and MF. We also include Nicastrin that is part of the gamma secretase complex and not known to be a peptidase.

The clan contains the following 17 members:

Amidase_3 AstE_AspA DUF2817 DUF4910 FGase Gamma_PGA_hydro Glycolytic Ncstrn_small Nicastrin Peptidase_M14 Peptidase_M17 Peptidase_M18 Peptidase_M20 Peptidase_M28 Peptidase_M42 Peptidase_M99 SpoIIP

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 and the UniProtKB sequence database. More...

View options

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
(62)
Full
(13527)
Representative proteomes UniProt
(67848)
RP15
(1948)
RP35
(7131)
RP55
(14067)
RP75
(23893)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(62)
Full
(13527)
Representative proteomes UniProt
(67848)
RP15
(1948)
RP35
(7131)
RP55
(14067)
RP75
(23893)
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
(62)
Full
(13527)
Representative proteomes UniProt
(67848)
RP15
(1948)
RP35
(7131)
RP55
(14067)
RP75
(23893)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_888 (release 4.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 62
Number in full: 13527
Average length of the domain: 192.4 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 50.9 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.8
Model length: 174
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Amidase_3 domain has been found. There are 27 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GH87 View 3D Structure Click here
A0A0H3GWG2 View 3D Structure Click here
A0A0H3GXU3 View 3D Structure Click here
I6Y4D2 View 3D Structure Click here
K0F561 View 3D Structure Click here
K0FF30 View 3D Structure Click here
L7N653 View 3D Structure Click here
O25464 View 3D Structure Click here
O32041 View 3D Structure Click here
P26365 View 3D Structure Click here
P26366 View 3D Structure Click here
P33772 View 3D Structure Click here
P36548 View 3D Structure Click here
P44493 View 3D Structure Click here
P50864 View 3D Structure Click here
P54525 View 3D Structure Click here
P57638 View 3D Structure Click here
P58698 View 3D Structure Click here
P63883 View 3D Structure Click here
Q02114 View 3D Structure Click here
Q06320 View 3D Structure Click here
Q0P8Y7 View 3D Structure Click here
Q2FXU3 View 3D Structure Click here
Q2FYD8 View 3D Structure Click here
Q328E8 View 3D Structure Click here
Q32CA4 View 3D Structure Click here
Q32DB8 View 3D Structure Click here
Q49Y70 View 3D Structure Click here
Q4L6X7 View 3D Structure Click here
Q5F6P7 View 3D Structure Click here
Q5HNS0 View 3D Structure Click here
Q89A33 View 3D Structure Click here
Q8ZMB9 View 3D Structure Click here
Q9CB75 View 3D Structure Click here
Q9CCX8 View 3D Structure Click here
Q9HT36 View 3D Structure Click here
Q9HUL7 View 3D Structure Click here
Q9K0V3 View 3D Structure Click here
Q9RMZ0 View 3D Structure Click here
X8F2Y6 View 3D Structure Click here