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124  structures 526  species 1  interaction 600  sequences 6  architectures

Family: SAM_adeno_trans (PF01887)

Summary: S-adenosyl-l-methionine hydroxide adenosyltransferase

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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-adenosyl-l-methionine hydroxide adenosyltransferase Provide feedback

This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme [1]. S-adenosyl-l-methionine hydroxide adenosyltransferases utilises a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion [2]. This family used to be known as DUF62.

Literature references

  1. Rao KN, Burley SK, Swaminathan S; , Proteins. 2008;70:572-577.: Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. PUBMED:17910070 EPMC:17910070

  2. Deng H, O'Hagan D; , Curr Opin Chem Biol. 2008;12:582-592.: The fluorinase, the chlorinase and the duf-62 enzymes. PUBMED:18675376 EPMC:18675376


This tab holds annotation information from the InterPro database.

InterPro entry IPR002747

Adenosyl-chloride synthase or chlorinase SalL mediates catalyses the halogenation of S-adenosyl-L-methionine (SAM) with chloride to generate 5'-chloro-5'-deoxyadenosine (5'-CIDA) and L-methionine [PUBMED:18059261]. The fluorinase FlA from Streptomyces cattleya is involved in the synthesis of fluorometabolites and has homology to SalL [PUBMED:18675376]. It catalyses the formation of a C-F bond by combining S-adenosyl-L-methionine (SAM) and fluoride to generate 5'-fluoro-5'-deoxyadenosine (5'-FDA) and L-methionine [PUBMED:17985882], but it can also function as a chlorinase [PUBMED:16370017].

This family also includes chlorinase MJ1651 from Methanocaldococcus jannaschii. Its protein structure is most closely related to the bacterial fluorinating enzyme; however, it may have different function [PUBMED:17910070].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(330)
Full
(600)
Representative proteomes UniProt
(2400)
NCBI
(3256)
Meta
(488)
RP15
(248)
RP35
(548)
RP55
(842)
RP75
(1196)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(330)
Full
(600)
Representative proteomes UniProt
(2400)
NCBI
(3256)
Meta
(488)
RP15
(248)
RP35
(548)
RP55
(842)
RP75
(1196)
Alignment:
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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
(330)
Full
(600)
Representative proteomes UniProt
(2400)
NCBI
(3256)
Meta
(488)
RP15
(248)
RP35
(548)
RP55
(842)
RP75
(1196)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Enright A
Previous IDs: DUF62;
Type: Family
Author: Enright A, Ouzounis C, Bateman A, Cerutti L
Number in seed: 330
Number in full: 600
Average length of the domain: 245.30 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 90.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.9 25.2
Noise cut-off 24.7 24.6
Model length: 236
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

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

SAM_adeno_trans

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 SAM_adeno_trans domain has been found. There are 124 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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