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464  structures 8379  species 0  interactions 193796  sequences 5385  architectures

Family: AMP-binding (PF00501)

Summary: AMP-binding enzyme

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

AMP-binding enzyme Provide feedback

No Pfam abstract.

Literature references

  1. Conti E, Franks NP, Brick P; , Structure 1996;4:287-298.: Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. PUBMED:8805533 EPMC:8805533


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000873

A number of prokaryotic and eukaryotic enzymes, which appear to act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity [ PUBMED:2118102 , PUBMED:2911486 , PUBMED:2254270 ]. This region is a Ser/Thr/Gly-rich domain that is further characterised by a conserved Pro-Lys-Gly triplet. The family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases [ PUBMED:8805533 , PUBMED:26473393 ].

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 ANL (CL0378), which has the following description:

This superfamily consists of enzymes including luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases as well as a plant auxin-responsive promoter family. The name ANL derives from from three of the subfamilies - Acyl-CoA synthetases, the NRPS adenylation domains, and the Luciferase enzymes [1]. Members of this superfamily catalyse the initial adenylation of a carboxylate to form an acyl-AMP intermediate, followed by a second partial reaction, most commonly the formation of a thioester [1].

The clan contains the following 4 members:

ACAS_N AMP-binding GH3 LuxE

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
(141)
Full
(193796)
Representative proteomes UniProt
(728633)
RP15
(22070)
RP35
(80240)
RP55
(178546)
RP75
(309504)
Jalview View  View  View  View  View  View  View 
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
(141)
Full
(193796)
Representative proteomes UniProt
(728633)
RP15
(22070)
RP35
(80240)
RP55
(178546)
RP75
(309504)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(141)
Full
(193796)
Representative proteomes UniProt
(728633)
RP15
(22070)
RP35
(80240)
RP55
(178546)
RP75
(309504)
Raw Stockholm Download     Download          
Gzipped 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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Eberhardt R
Number in seed: 141
Number in full: 193796
Average length of the domain: 383.40 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 51.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.9 29.9
Trusted cut-off 29.9 29.9
Noise cut-off 29.8 29.8
Model length: 424
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

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

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 AMP-binding domain has been found. There are 464 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
A0A061AD00 View 3D Structure Click here
A0A061AD00 View 3D Structure Click here
A0A096PQY2 View 3D Structure Click here
A0A096PZ50 View 3D Structure Click here
A0A096S078 View 3D Structure Click here
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A0A0R0HAN2 View 3D Structure Click here
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A0A0R0HQ49 View 3D Structure Click here
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A0A0R0JS26 View 3D Structure Click here
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A0A0R4IRL6 View 3D Structure Click here
A0A1D6DQH1 View 3D Structure Click here
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A0A1D6H286 View 3D Structure Click here
A0A1D6H9J3 View 3D Structure Click here
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A0A1D6I3L3 View 3D Structure Click here
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A0A1D6JIH7 View 3D Structure Click here
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A0A1D6K083 View 3D Structure Click here
A0A1D6KA74 View 3D Structure Click here
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A0A1D6KNK6 View 3D Structure Click here
A0A1D6KNL0 View 3D Structure Click here
A0A1D6KW34 View 3D Structure Click here
A0A1D6L8C0 View 3D Structure Click here
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A0A1D6LWI0 View 3D Structure Click here
A0A1D6MDN1 View 3D Structure Click here
A0A1D6MEX0 View 3D Structure Click here
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A0A1D6Q7M3 View 3D Structure Click here
A0A1D6QAL5 View 3D Structure Click here
A0A1D6QD94 View 3D Structure Click here
A0A1D6QGV9 View 3D Structure Click here
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A0A1D8PU56 View 3D Structure Click here
A0A1X7YEZ5 View 3D Structure Click here
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A0A2R8QE30 View 3D Structure Click here
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