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116  structures 4062  species 3  interactions 12240  sequences 79  architectures

Family: Amidase (PF01425)

Summary: Amidase

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This is the Wikipedia entry entitled "Amidase". More...

Amidase Edit Wikipedia article

amidase
Identifiers
EC number 3.5.1.4
CAS number 9012-56-0
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
PDB 1m22 EBI.jpg
x-ray structure of native peptide amidase from stenotrophomonas maltophilia at 1.4 a
Identifiers
Symbol Amidase
Pfam PF01425
InterPro IPR000120
PROSITE PDOC00494
SCOP 1ocm
SUPERFAMILY 1ocm
OPM superfamily 72
OPM protein 1mt5

In enzymology, an amidase (EC 3.5.1.4, acylamidase, acylase (misleading), amidohydrolase (ambiguous), deaminase (ambiguous), fatty acylamidase, N-acetylaminohydrolase (ambiguous)) is an enzyme that catalyzes the hydrolysis of an amide:

Amide hydrolysis Amidase.png


Thus, the two substrates of this enzyme are monocarboxylic acid amide and H2O, whereas its two products are monocarboxylate and NH3.

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is acylamide amidohydrolase. Other names in common use include acylamidase, acylase, amidohydrolase, deaminase, fatty acylamidase, and N-acetylaminohydrolase. This enzyme participates in 6 metabolic pathways: urea cycle and metabolism of amino groups, phenylalanine metabolism, tryptophan metabolism, cyanoamino acid metabolism, benzoate degradation via coa ligation, and styrene degradation.

Amidases contain a conserved stretch of approximately 130 amino acids known as the AS sequence. They are widespread, being found in both prokaryotes and eukaryotes. AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2), although the family has diverged widely with regard to substrate specificity and function. Nonetheless, these enzymes maintain a core alpha/beta/alpha structure, where the topologies of the N- and C-terminal halves are similar. AS enzymes characteristically have a highly conserved C-terminal region rich in serine and glycine residues, but devoid of aspartic acid and histidine residues, therefore they differ from classical serine hydrolases. These enzymes possess a unique, highly conserved Ser-Ser-Lys catalytic triad used for amide hydrolysis, although the catalytic mechanism for acyl-enzyme intermediate formation can differ between enzymes.[1]

Examples of AS signature-containing enzymes include:

  • Subunit A of Glu-tRNA(Gln) amidotransferase,[4]a heterotrimeric enzyme that catalyses the formation of Gln-tRNA(Gln) by the transamidation of misacylated Glu-tRNA(Gln) via amidolysis of glutamine.

Structural studies[edit]

As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 2PLQ and 2UXY.

References[edit]

  1. ^ a b Valiña AL, Mazumder-Shivakumar D, Bruice TC (December 2004). "Probing the Ser-Ser-Lys catalytic triad mechanism of peptide amidase: computational studies of the ground state, transition state, and intermediate". Biochemistry 43 (50): 15657–72. doi:10.1021/bi049025r. PMID 15595822. 
  2. ^ Wei BQ, Mikkelsen TS, McKinney MK, Lander ES, Cravatt BF (December 2006). "A second fatty acid amide hydrolase with variable distribution among placental mammals". J. Biol. Chem. 281 (48): 36569–78. doi:10.1074/jbc.M606646200. PMID 17015445. 
  3. ^ Shin S, Lee TH, Ha NC, Koo HM, Kim SY, Lee HS, Kim YS, Oh BH (June 2002). "Structure of malonamidase E2 reveals a novelSer-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature". EMBO J. 21 (11): 2509–16. doi:10.1093/emboj/21.11.2509. PMC 126024. PMID 12032064. 
  4. ^ Kwak JH, Shin K, Woo JS, Kim MK, Kim SI, Eom SH, Hong KW (December 2002). "Expression, purification, and crystallization of glutamyl-tRNA(Gln) specific amidotransferase from Bacillus stearothermophilus". Mol. Cells 14 (3): 374–81. PMID 12521300. 

Further reading[edit]

  • Bray HG, James SP, Raffan IM, Ryman BE and Thorpe WV (1949). "The fate of certain organic acids and amides in the rabbit. 7. An amidase of rabbit liver". Biochem. J. 44: 618–625. 
  • Bray HG, James SP, Thorpe WV and Wasdell MR (1950). "The fate of certain organic acids and amides in the rabbit. 11 Further observations on the hydrolysis of amides by tissue extracts". Biochem. J. 47: 294–299. 


This article incorporates text from the public domain Pfam and InterPro IPR000120

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

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Amidase Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000120

Amidase signature (AS) enzymes are a large group of hydrolytic enzymes that contain a conserved stretch of approximately 130 amino acids known as the AS sequence. They are widespread, being found in both prokaryotes and eukaryotes. AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2), although the family has diverged widely with regard to substrate specificity and function. Nonetheless, these enzymes maintain a core alpha/beta/alpha structure, where the topologies of the N- and C-terminal halves are similar. AS enzymes characteristically have a highly conserved C-terminal region rich in serine and glycine residues, but devoid of aspartic acid and histidine residues, therefore they differ from classical serine hydrolases. These enzymes posses a unique, highly conserved Ser-Ser-Lys catalytic triad used for amide hydrolysis, although the catalytic mechanism for acyl-enzyme intermediate formation can differ between enzymes [PUBMED:15595822].

Examples of AS enzymes include:

  • Peptide amidase (Pam) [PUBMED:15595822], which catalyses the hydrolysis of the C-terminal amide bond of peptides.
  • Fatty acid amide hydrolases [PUBMED:17015445], which hydrolyse fatty acid amid substrates (e.g. cannabinoid anandamide and sleep-inducing oleamide), thereby controlling the level and duration of signalling induced by this diverse class of lipid transmitters.
  • Malonamidase E2 [PUBMED:12032064], which catalyses the hydrolysis of malonamate into malonate and ammonia, and which is involved in the transport of fixed nitrogen from bacteroids to plant cells in symbiotic nitrogen metabolism.
  • Subunit A of Glu-tRNA(Gln) amidotransferase [PUBMED:12521300],a heterotrimeric enzyme that catalyses the formation of Gln-tRNA(Gln) by the transamidation of misacylated Glu-tRNA(Gln) via amidolysis of glutamine.

Gene Ontology

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Domain organisation

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Alignments

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(9300)
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RP35
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  Seed
(44)
Full
(12240)
Representative proteomes NCBI
(11144)
Meta
(9300)
RP15
(1337)
RP35
(2800)
RP55
(4004)
RP75
(4833)
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  Seed
(44)
Full
(12240)
Representative proteomes NCBI
(11144)
Meta
(9300)
RP15
(1337)
RP35
(2800)
RP55
(4004)
RP75
(4833)
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

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Curation and family details

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Seed source: Pfam-B_191 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 44
Number in full: 12240
Average length of the domain: 393.40 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 83.65 %

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 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 19.9 20.0
Model length: 441
Family (HMM) version: 16
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Species distribution

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Interactions

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

Glu-tRNAGln GatB_N Amidase

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 domain has been found. There are 116 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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