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19  structures 1523  species 1  interaction 1798  sequences 11  architectures

Family: AdoMet_dc (PF02675)

Summary: S-adenosylmethionine decarboxylase

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This is the Wikipedia entry entitled "Adenosylmethionine decarboxylase". More...

Adenosylmethionine decarboxylase Edit Wikipedia article

adenosylmethionine decarboxylase
Identifiers
EC number 4.1.1.50
CAS number 9036-20-8
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
adenosylmethionine decarboxylase 1
Identifiers
Symbol AMD1
Entrez 262
HUGO 457
OMIM 180980
RefSeq NM_001634
UniProt P17707
Other data
Locus Chr. 6 q21-q22
AdoMet decarboxylase
PDB 1tlu EBI.jpg
crystal structure of thermotoga maritima s-adenosylmethionine decarboxylase
Identifiers
Symbol AdoMet_dc
Pfam PF02675
InterPro IPR003826

Adenosylmethionine decarboxylase is an enzyme that catalyzes the conversion of S-adenosyl methionine to S-adenosylmethioninamine. Polyamines such as spermidine and spermine are essential for cellular growth under most conditions, being implicated in a large number of cellular processes including DNA, RNA and protein synthesis. S-adenosylmethionine decarboxylase (AdoMetDC) plays an essential regulatory role in the polyamine biosynthetic pathway by generating the n-propylamine residue required for the synthesis of spermidine and spermine from putrescein.[1][2] Unlike many amino acid decarboxylases AdoMetDC uses a covalently bound pyruvate residue as a cofactor rather than the more common pyridoxal 5'-phosphate. These proteins can be divided into two main groups which show little sequence similarity either to each other, or to other pyruvoyl-dependent amino acid decarboxylases: class I enzymes found in bacteria and archaea, and class II enzymes found in eukaryotes. In both groups the active enzyme is generated by the post-translational autocatalytic cleavage of a precursor protein. This cleavage generates the pyruvate precursor from an internal serine residue and results in the formation of two non-identical subunits termed alpha and beta which form the active enzyme.

References[edit]

  1. ^ van Poelje PD, Snell EE (1990). "Pyruvoyl-dependent enzymes". Annu. Rev. Biochem. 59: 29–59. doi:10.1146/annurev.bi.59.070190.000333. PMID 2197977. 
  2. ^ Pegg AE, Xiong H, Feith DJ, Shantz LM (November 1998). "S-adenosylmethionine decarboxylase: structure, function and regulation by polyamines". Biochem. Soc. Trans. 26 (4): 580–6. PMID 10047786. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR003826

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.

S-adenosylmethionine decarboxylase Provide feedback

This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesised as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity [1,2].

Literature references

  1. Li YF, Hess S, Pannell LK, White Tabor C, Tabor H; , Proc Natl Acad Sci U S A 2001;98:10578-10583.: In vivo mechanism-based inactivation of S-adenosylmethionine decarboxylases from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae. PUBMED:11526206 EPMC:11526206

  2. Sekowska A, Coppee JY, Le Caer JP, Martin-Verstraete I, Danchin A; , Mol Microbiol 2000;36:1135-1147.: S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts. PUBMED:10844697 EPMC:10844697


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003826

Polyamines such as spermidine and spermine are essential for cellular growth under most conditions, being implicated in a large number of cellular processes including DNA, RNA and protein synthesis. S-adenosylmethionine decarboxylase (AdoMetDC) plays an essential regulatory role in the polyamine biosynthetic pathway by generating the n-propylamine residue required for the synthesis of spermidine and spermine from putrescein [PUBMED:2197977, PUBMED:10047786]. Unlike many amino acid decarboxylases AdoMetDC uses a covalently bound pyruvate residue as a cofactor rather than the more common pyridoxal 5'-phosphate. These proteins can be divided into two main groups which show little sequence similarity either to each other, or to other pyruvoyl-dependent amino acid decarboxylases: class I enzymes found in bacteria and archaea, and class II enzymes found in eukaryotes. In both groups the active enzyme is generated by the post-translational autocatalytic cleavage of a precursor protein. This cleavage generates the pyruvate precursor from an internal serine residue and results in the formation of two non-identical subunits termed alpha and beta which form the active enzyme.

Members of this family are related to the amino terminus of Escherichia coli S-adenosylmethionine decarboxylase.

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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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
(134)
Full
(1798)
Representative proteomes NCBI
(1159)
Meta
(1636)
RP15
(183)
RP35
(309)
RP55
(389)
RP75
(460)
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Format an alignment

  Seed
(134)
Full
(1798)
Representative proteomes NCBI
(1159)
Meta
(1636)
RP15
(183)
RP35
(309)
RP55
(389)
RP75
(460)
Alignment:
Format:
Order:
Sequence:
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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
(134)
Full
(1798)
Representative proteomes NCBI
(1159)
Meta
(1636)
RP15
(183)
RP35
(309)
RP55
(389)
RP75
(460)
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.

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: COG1586
Previous IDs: DUF206; AdoMetDC;
Type: Family
Author: Mian N, Bateman A, Moxon SJ
Number in seed: 134
Number in full: 1798
Average length of the domain: 119.90 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 60.28 %

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 25.0 25.0
Trusted cut-off 27.6 27.3
Noise cut-off 22.5 22.2
Model length: 106
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

AdoMet_dc

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 AdoMet_dc domain has been found. There are 19 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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