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14  structures 798  species 0  interactions 954  sequences 3  architectures

Family: AstB (PF04996)

Summary: Succinylarginine dihydrolase

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.

Succinylarginine dihydrolase Provide feedback

This enzyme transforms N(2)-succinylglutamate into succinate and glutamate. This is the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway.

Literature references

  1. Schneider BL, Kiupakis AK, Reitzer LJ; , J Bacteriol 1998;180:4278-4286.: Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. PUBMED:9696779 EPMC:9696779


This tab holds annotation information from the InterPro database.

InterPro entry IPR007079

Succinylarginine dihydrolase (AstB) transforms N(2)-succinylglutamate into succinate and glutamate. This enzyme is the second in the five-step ammonia-producing arginine succinyltransferase pathway, the major pathway in Escherichia coli and in other related bacteria for arginine catabolism as a sole nitrogen source. AstB assumes a five-stranded alpha/beta propeller structure, placing it in the amidinotransferase (AT) superfamily of proteins, which are characterised by their Cys-His-Glu active site triad [ PUBMED:15703173 ].

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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Pfam Clan

This family is a member of clan GME (CL0197), which has the following description:

This superfamily contains a number of related enzymes such as AstB, peptidyl-arginine deiminase, arginine deiminase and amidinotransferase [1,2].

The clan contains the following 6 members:

ADI AstB DDAH_eukar eIF-6 PAD PAD_porph

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
(43)
Full
(954)
Representative proteomes UniProt
(7182)
RP15
(95)
RP35
(367)
RP55
(970)
RP75
(2136)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(43)
Full
(954)
Representative proteomes UniProt
(7182)
RP15
(95)
RP35
(367)
RP55
(970)
RP75
(2136)
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
(43)
Full
(954)
Representative proteomes UniProt
(7182)
RP15
(95)
RP35
(367)
RP55
(970)
RP75
(2136)
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: COG3724
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 43
Number in full: 954
Average length of the domain: 424.1 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 98.97 %

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 27.0 27.0
Trusted cut-off 40.3 40.3
Noise cut-off 20.2 19.9
Model length: 443
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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The tree shows the occurrence of this domain across different species. 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 AstB domain has been found. There are 14 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
A0A0H3GSQ9 View 3D Structure Click here
A0A0H3GVX4 View 3D Structure Click here
A0KMV4 View 3D Structure Click here
A1S572 View 3D Structure Click here
A3QF43 View 3D Structure Click here
A4XWE6 View 3D Structure Click here
A5V3M9 View 3D Structure Click here
A8AHD7 View 3D Structure Click here
A8H2S2 View 3D Structure Click here
A9AD18 View 3D Structure Click here
A9MFF9 View 3D Structure Click here
B1KNK9 View 3D Structure Click here
B2JCG4 View 3D Structure Click here
B2VEK6 View 3D Structure Click here
C3JXY6 View 3D Structure Click here
O50175 View 3D Structure Click here
P76216 View 3D Structure Click here
Q080J1 View 3D Structure Click here
Q12LR7 View 3D Structure Click here
Q141D2 View 3D Structure Click here
Q15TB5 View 3D Structure Click here
Q1DDF6 View 3D Structure Click here
Q1GRR9 View 3D Structure Click here
Q1QTQ8 View 3D Structure Click here
Q2G9Z6 View 3D Structure Click here
Q2SKP0 View 3D Structure Click here
Q2Y8M6 View 3D Structure Click here
Q32G87 View 3D Structure Click here
Q3ID31 View 3D Structure Click here
Q4K838 View 3D Structure Click here
Q5DZ79 View 3D Structure Click here
Q5NNB4 View 3D Structure Click here
Q5QWI1 View 3D Structure Click here
Q5ZUT4 View 3D Structure Click here
Q63SD8 View 3D Structure Click here
Q6FCP9 View 3D Structure Click here
Q6LJR6 View 3D Structure Click here
Q7ADE7 View 3D Structure Click here
Q7N2H0 View 3D Structure Click here
Q7NXX6 View 3D Structure Click here