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302  structures 8181  species 0  interactions 25296  sequences 138  architectures

Family: Aminotran_4 (PF01063)

Summary: Amino-transferase class IV

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Amino-transferase class IV Provide feedback

The D-amino acid transferases (D-AAT) are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity.

Literature references

  1. Sugio S, Petsko GA, Manning JM, Soda K, Ringe D; , Biochemistry 1995;34:9661-9669.: Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity. PUBMED:7626635 EPMC:7626635

  2. Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H; , J Biochem 1997;121:637-641.: Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution. PUBMED:9163511 EPMC:9163511


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001544

Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [ PUBMED:1644759 ] into subfamilies.

This entry represents a subfamily of aminotransferases, called class-IV, with currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [ PUBMED:7626635 , PUBMED:9163511 ].

This group also includes transaminase htyB from Aspergillus rugulosus , which is one of the enzymes required for the biosynthesis of the antifungal agent echinocandin B. HtyB catalyses the production of L-homotyrosine from the intermediate 2-oxo-4-(4-hydroxybenzyl)butanoic acid [ PUBMED:22998630 ]. Also included in this group is branched-chain amino acid aminotransferase gloG from the yeast Glarea lozoyensis , which is required for biosynthesis of the mycotoxin pneumocandin, also a lipohexapeptide of the echinocandin family [ PUBMED:27705900 ].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(69)
Full
(25296)
Representative proteomes UniProt
(102355)
RP15
(3231)
RP35
(11513)
RP55
(23936)
RP75
(39732)
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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
(69)
Full
(25296)
Representative proteomes UniProt
(102355)
RP15
(3231)
RP35
(11513)
RP55
(23936)
RP75
(39732)
Alignment:
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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
(69)
Full
(25296)
Representative proteomes UniProt
(102355)
RP15
(3231)
RP35
(11513)
RP55
(23936)
RP75
(39732)
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: Pfam-B_607 (release 3.0)
Previous IDs: AA_transferase_C4;aminotran_4;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 69
Number in full: 25296
Average length of the domain: 227.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 67.78 %

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 28.5 28.5
Trusted cut-off 28.5 28.5
Noise cut-off 28.4 28.4
Model length: 223
Family (HMM) version: 21
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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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 Aminotran_4 domain has been found. There are 302 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
A0A096RBT2 View 3D Structure Click here
A0A0P0XXH0 View 3D Structure Click here
A0A0R0H563 View 3D Structure Click here
A0A0R0INS4 View 3D Structure Click here
A0A1D6E3I5 View 3D Structure Click here
A0A1D6H505 View 3D Structure Click here
A0A1D6JUA3 View 3D Structure Click here
A0A1D6K3R8 View 3D Structure Click here
A0A1D6K833 View 3D Structure Click here
A0A1D6PM16 View 3D Structure Click here
A0A1D8PH42 View 3D Structure Click here
A0A1D8PKB9 View 3D Structure Click here
A4I2W8 View 3D Structure Click here
A4I9Z9 View 3D Structure Click here
C6T8V8 View 3D Structure Click here
E9QCQ6 View 3D Structure Click here
I1J9H2 View 3D Structure Click here
I1JRF2 View 3D Structure Click here
I1JTU1 View 3D Structure Click here
I1K9A2 View 3D Structure Click here
I1LV30 View 3D Structure Click here
K7KIU8 View 3D Structure Click here
K7KT64 View 3D Structure Click here
K7L2J8 View 3D Structure Click here
K7L2K0 View 3D Structure Click here
K7L581 View 3D Structure Click here
K7L583 View 3D Structure Click here
K7LJM5 View 3D Structure Click here
K7MMK0 View 3D Structure Click here
K7N3H2 View 3D Structure Click here
O14370 View 3D Structure Click here
O15382 View 3D Structure Click here
O35854 View 3D Structure Click here
O35855 View 3D Structure Click here
O42951 View 3D Structure Click here
P0AB80 View 3D Structure Click here
P24288 View 3D Structure Click here
P28305 View 3D Structure Click here
P38891 View 3D Structure Click here
P47176 View 3D Structure Click here
P54687 View 3D Structure Click here
P54688 View 3D Structure Click here
P54690 View 3D Structure Click here
P9WQ75 View 3D Structure Click here
Q03266 View 3D Structure Click here
Q0DJP6 View 3D Structure Click here
Q0E243 View 3D Structure Click here
Q0E2C2 View 3D Structure Click here
Q2FXI0 View 3D Structure Click here
Q2G097 View 3D Structure Click here
Q2G0M4 View 3D Structure Click here
Q4E589 View 3D Structure Click here
Q54N47 View 3D Structure Click here
Q58414 View 3D Structure Click here
Q5A0H4 View 3D Structure Click here
Q5NAM3 View 3D Structure Click here
Q5RHB8 View 3D Structure Click here
Q6AT43 View 3D Structure Click here
Q79FW0 View 3D Structure Click here
Q7XPR5 View 3D Structure Click here
Q8GRH8 View 3D Structure Click here
Q8H7T7 View 3D Structure Click here
Q8IKP7 View 3D Structure Click here
Q8L493 View 3D Structure Click here
Q8VZN6 View 3D Structure Click here
Q8W0Z7 View 3D Structure Click here
Q93Y32 View 3D Structure Click here
Q9ASR4 View 3D Structure Click here
Q9FYA6 View 3D Structure Click here
Q9LE06 View 3D Structure Click here
Q9LPM8 View 3D Structure Click here
Q9LPM9 View 3D Structure Click here
Q9M401 View 3D Structure Click here
Q9M439 View 3D Structure Click here
Q9VYD5 View 3D Structure Click here
Q9XXD8 View 3D Structure Click here