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0  structures 204  species 0  interactions 235  sequences 30  architectures

Family: Amidase_5 (PF05382)

Summary: Bacteriophage peptidoglycan hydrolase

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

N-acetylmuramoyl-L-alanine amidase
Identifiers
EC number 3.5.1.28
CAS number 9013-25-6
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Amidase_2
PDB 1sk4 EBI.jpg
crystal structure of the c-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein ialpha
Identifiers
Symbol Amidase_2
Pfam PF01510
InterPro IPR002502
SCOP 1lba
SUPERFAMILY 1lba
OPM superfamily 438
OPM protein 1sk4
Amidase_3
PDB 1jwq EBI.jpg
structure of the catalytic domain of cwlv, n-acetylmuramoyl-l-alanine amidase from bacillus(paenibacillus) polymyxa var.colistinus
Identifiers
Symbol Amidase_3
Pfam PF01520
Pfam clan CL0035
InterPro IPR002508
SCOP 1jwq
SUPERFAMILY 1jwq
Amidase_5
Identifiers
Symbol Amidase_5
Pfam PF05382
Pfam clan CL0125
InterPro IPR008044
Amidase02_C
Identifiers
Symbol Amidase02_C
Pfam PF12123
InterPro IPR021976

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, N-acetylmuramoyl-L-alanine amidase type I, and N-acetylmuramoyl-L-alanine amidase type II. This enzyme participates in peptidoglycan biosynthesis. Autolysins and some phage lysins are examples of N-acetylmuramoyl-L-alanine amidases.

See also

References

  • Campbell JN; Dierickx, L; Coyette, J; Leyh-Bouille, M; Guinand, M; 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 (1): 213–22. doi:10.1021/bi00829a031. PMID 5777325. 
  • Herbold DR, Glaser L (1975). "Interaction of N-acetylmuramic acid L-alanine amidase with cell wall polymers". J. Biol. Chem. 250 (18): 7231–8. PMID 809432. 
  • Herbold DR, Glaser L (1975). "Bacillus subtilis N-acetylmuramic acid L-alanine amidase". J. Biol. Chem. 250 (5): 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 (6): 1171–8. doi:10.1099/00221287-128-6-1171. PMID 6126517. 

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.

Bacteriophage peptidoglycan hydrolase Provide feedback

At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 O03979 has been shown to be a N-acetylmuramoyl-L-alanine amidase [1]. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids [2,3]. This family appears to be related to PF00877.

Literature references

  1. Garcia P, Mendez E, Garcia E, Ronda C, Lopez R; , J Bacteriol 1984;159:793-796.: Biochemical characterization of a murein hydrolase induced by bacteriophage Dp-1 in Streptococcus pneumoniae: comparative study between bacteriophage-associated lysin and the host amidase. PUBMED:6146601 EPMC:6146601

  2. Sheehan MM, Garcia JL, Lopez R, Garcia P; , Mol Microbiol 1997;25:717-725.: The lytic enzyme of the pneumococcal phage Dp-1: a chimeric lysin of intergeneric origin. PUBMED:9379901 EPMC:9379901

  3. Garcia E, Garcia JL, Garcia P, Arraras A, Sanchez-Puelles JM, Lopez R; , Proc Natl Acad Sci U S A 1988;85:914-918.: Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages. PUBMED:3422470 EPMC:3422470


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008044

This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase [PUBMED:6146601]. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [PUBMED:9379901, PUBMED:3422470].

Domain organisation

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Alignments

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  Seed
(8)
Full
(235)
Representative proteomes NCBI
(361)
Meta
(31)
RP15
(13)
RP35
(19)
RP55
(26)
RP75
(32)
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  Seed
(8)
Full
(235)
Representative proteomes NCBI
(361)
Meta
(31)
RP15
(13)
RP35
(19)
RP55
(26)
RP75
(32)
Alignment:
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  Seed
(8)
Full
(235)
Representative proteomes NCBI
(361)
Meta
(31)
RP15
(13)
RP35
(19)
RP55
(26)
RP75
(32)
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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.

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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: Pfam-B_6845 (Pfam7.8)
Previous IDs: none
Type: Family
Author: Studholme DJ, Garcia E
Number in seed: 8
Number in full: 235
Average length of the domain: 134.80 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 32.91 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 145
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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