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143  structures 18991  species 3  interactions 38955  sequences 28  architectures

Family: Semialdhyde_dhC (PF02774)

Summary: Semialdehyde dehydrogenase, dimerisation domain

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

This is the Wikipedia entry entitled "Aspartate-semialdehyde dehydrogenase". More...

Aspartate-semialdehyde dehydrogenase Edit Wikipedia article

aspartate-semialdehyde dehydrogenase
Identifiers
EC number 1.2.1.11
CAS number 9000-98-0
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

In enzymology, an aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) is an enzyme that is very important in the biosynthesis of amino acids in prokaryotes, fungi, and some higher plants. It forms an early branch point in the metabolic pathway forming lysine, methionine, leucine and isoleucine from aspartate. This pathway also produces diaminopimelate which plays an essential role in bacterial cell wall formation. There is particular interest in ASADH as disabling this enzyme proves fatal to the organism giving rise to the possibility of a new class of antibiotics, fungicides, and herbicides aimed at inhibiting it.

The enzyme catalyzes the reversible chemical reaction

L-aspartate 4-semialdehyde + phosphate + NADP+ \rightleftharpoons L-4-aspartyl phosphate + NADPH + H+

The 3 substrates of this enzyme are L-aspartate 4-semialdehyde, phosphate, and NADP+, whereas its 3 products are L-4-aspartyl phosphate, NADPH, and H+. In physiological conditions however, the reaction runs in the opposite direction. This enzyme belongs to the family of oxidoreductases, specifically those acting on the aldehyde or oxo group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is L-aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating). Other names in common use include aspartate semialdehyde dehydrogenase, aspartic semialdehyde dehydrogenase, L-aspartate-beta-semialdehyde:NADP+ oxidoreductase, (phosphorylating), aspartic beta-semialdehyde dehydrogenase, and ASA dehydrogenase. This enzyme participates in glycine, serine and threonine metabolism and lysine biosynthesis.

Aspartate-semialdehyde dehydrogenase may be cis-regulated by an Asd RNA motif found in the 5' UTR of some Asd genes.

Protein families

Semialdehyde dehydrogenase, dimerisation domain
Identifiers
Symbol Semialdhyde_dhC
Pfam PF02774
Pfam clan CL0139
InterPro IPR012280

This domain contains both N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), which is involved in arginine biosynthesis, and aspartate-semialdehyde dehydrogenase,[1] an enzyme involved in the biosynthesis of various amino acids from aspartate. It also contains the yeast and fungal Arg5,6 protein, which is cleaved into the enzymes N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase. These are also involved in arginine biosynthesis. All proteins in this entry contain a dimerisation domain of semialdehyde dehydrogenase.

Structural studies

As of late 2007, 24 structures have been solved for this class of enzymes, with PDB accession codes 1BRM, 1GL3, 1MB4, 1MC4, 1NWC, 1NWH, 1NX6, 1OZA, 1PQP, 1PQU, 1PR3, 1PS8, 1PU2, 1Q2X, 1T4B, 1T4D, 1TA4, 1TB4, 1YS4, 2EP5, 2GYY, 2GZ1, 2GZ2, and 2GZ3.

References

  • BLACK S, WRIGHT NG (1955). "Aspartic beta-semialdehyde dehydrogenase and aspartic beta-semialdehyde". J. Biol. Chem. 213 (1): 39–50. PMID 14353904. 
  • Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd ed., vol. 7, Academic Press, New York, 1963, p. 203-221.


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Semialdehyde dehydrogenase, dimerisation domain Provide feedback

This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase.

Literature references

  1. Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R; , J Mol Biol 1999;289:991-1002.: Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. PUBMED:10369777 EPMC:10369777


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012280

This domain contains N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), which is involved in arginine biosynthesis, and aspartate-semialdehyde dehydrogenase [PUBMED:10369777], an enzyme involved in the biosynthesis of various amino acids from aspartate. It also contains the yeast and fungal Arg5,6 protein, which is cleaved into the enzymes N-acety-gamma-glutamyl-phosphate reductase and acetylglutamate kinase. These are also involved in arginine biosynthesis. All proteins in this entry contain a dimerisation domain of semialdehyde dehydrogenase.

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 GADPH_aa-bio_dh (CL0139), which has the following description:

This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids. It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.

The clan contains the following 2 members:

Gp_dh_C Semialdhyde_dhC

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(32)
Full
(38955)
Representative proteomes NCBI
(15597)
Meta
(4228)
RP15
(661)
RP35
(1749)
RP55
(2664)
RP75
(3476)
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Format an alignment

  Seed
(32)
Full
(38955)
Representative proteomes NCBI
(15597)
Meta
(4228)
RP15
(661)
RP35
(1749)
RP55
(2664)
RP75
(3476)
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
(32)
Full
(38955)
Representative proteomes NCBI
(15597)
Meta
(4228)
RP15
(661)
RP35
(1749)
RP55
(2664)
RP75
(3476)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_1079 (release 3.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 32
Number in full: 38955
Average length of the domain: 174.40 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 50.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 184
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

Semialdhyde_dhC Semialdhyde_dh Semialdhyde_dh

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 Semialdhyde_dhC domain has been found. There are 143 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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