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75  structures 7068  species 0  interactions 11471  sequences 79  architectures

Family: ATP-grasp_2 (PF08442)

Summary: ATP-grasp domain

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.

ATP-grasp domain Provide feedback

No Pfam abstract.

Literature references

  1. Galperin MY, Koonin EV; , Protein Sci 1997;6:2639-2643.: A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. PUBMED:9416615 EPMC:9416615


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013650

The ATP-grasp superfamily currently includes 17 groups of enzymes, catalysing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule [ PUBMED:9416615 ]. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination [ PUBMED:7939684 ].

The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site [ PUBMED:8804825 ]. The fold is characterised by two alpha-beta subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes [ PUBMED:7862655 ].

The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases ( EC ).

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 ATP-grasp (CL0179), which has the following description:

The ATP-grasp domain is found in a wide variety of carboxylate-amine/thiol ligases [1]. It is composed of two subdomains, with ATP being bound in the cleft between the two.

The clan contains the following 26 members:

ATP-grasp ATP-grasp_2 ATP-grasp_3 ATP-grasp_4 ATP-grasp_5 ATP-grasp_6 ATPgrasp_ST ATPgrasp_Ter ATPgrasp_TupA ATPgrasp_YheCD CP_ATPgrasp_1 CP_ATPgrasp_2 CPSase_L_D2 D123 Dala_Dala_lig_C DUF1297 GARS_A GSH-S_ATP GSP_synth Ins134_P3_kin PPDK_N R2K_2 R2K_3 RimK Synapsin_C TTL

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
(19)
Full
(11471)
Representative proteomes UniProt
(43211)
RP15
(1822)
RP35
(5276)
RP55
(10865)
RP75
(17601)
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
(19)
Full
(11471)
Representative proteomes UniProt
(43211)
RP15
(1822)
RP35
(5276)
RP55
(10865)
RP75
(17601)
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
(19)
Full
(11471)
Representative proteomes UniProt
(43211)
RP15
(1822)
RP35
(5276)
RP55
(10865)
RP75
(17601)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 19
Number in full: 11471
Average length of the domain: 197.70 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 46.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.5 29.5
Trusted cut-off 29.5 29.5
Noise cut-off 29.4 29.4
Model length: 202
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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 ATP-grasp_2 domain has been found. There are 75 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
A0A1D6HDG8 View 3D Structure Click here
A0A1D6LT95 View 3D Structure Click here
A0A1D6M043 View 3D Structure Click here
A0A1D6PN41 View 3D Structure Click here
A0A1D6Q567 View 3D Structure Click here
A0A1D8PTB5 View 3D Structure Click here
A0A2R8Q4D3 View 3D Structure Click here
A0A2R8Q7E9 View 3D Structure Click here
A0JT43 View 3D Structure Click here
A0KJK9 View 3D Structure Click here
A0LIY8 View 3D Structure Click here
A0LRU4 View 3D Structure Click here
A0R3M4 View 3D Structure Click here
A1APQ8 View 3D Structure Click here
A1AVI3 View 3D Structure Click here
A1AZH7 View 3D Structure Click here
A1BE51 View 3D Structure Click here
A1KAU3 View 3D Structure Click here
A1R3M0 View 3D Structure Click here
A1S5I0 View 3D Structure Click here
A1SMQ5 View 3D Structure Click here
A1SWX6 View 3D Structure Click here
A1TEP3 View 3D Structure Click here
A1TW81 View 3D Structure Click here
A1UL96 View 3D Structure Click here
A1UQV9 View 3D Structure Click here
A1VUC0 View 3D Structure Click here
A1WD26 View 3D Structure Click here
A1WLG5 View 3D Structure Click here
A1WZ92 View 3D Structure Click here
A3DLR9 View 3D Structure Click here
A3MZH0 View 3D Structure Click here
A3QDH6 View 3D Structure Click here
A4FP60 View 3D Structure Click here
A4G230 View 3D Structure Click here
A4ID83 View 3D Structure Click here
A4SDL6 View 3D Structure Click here
A4VKQ1 View 3D Structure Click here
A4XBE5 View 3D Structure Click here
A4XV90 View 3D Structure Click here