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286  structures 5328  species 3  interactions 25691  sequences 74  architectures

Family: AA_kinase (PF00696)

Summary: Amino acid kinase family

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This is the Wikipedia entry entitled "Amino acid kinase". More...

Amino acid kinase Edit Wikipedia article

AA_kinase
PDB 2bty EBI.jpg
acetylglutamate kinase from thermotoga maritima complexed with its inhibitor arginine
Identifiers
Symbol AA_kinase
Pfam PF00696
InterPro IPR001048
PROSITE PDOC00289
SCOP 1e19
SUPERFAMILY 1e19

In molecular biology, the amino acid kinase domain is a protein domain. It is found in protein kinases with various specificities, including the aspartate, glutamate and uridylate kinase families. In prokaryotes and plants the synthesis of the essential amino acids lysine and threonine is predominantly regulated by feed-back inhibition of aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). In Escherichia coli, thrA, metLM, and lysC encode aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively.[1] The lysine-sensitive isoenzyme of aspartate kinase from spinach leaves has a subunit composition of 4 large and 4 small subunits.[2]

In plants although the control of carbon fixation and nitrogen assimilation has been studied in detail, relatively little is known about the regulation of carbon and nitrogen flow into amino acids. The metabolic regulation of expression of an Arabidopsis thaliana aspartate kinase/homoserine dehydrogenase (AK/HSD) gene, which encodes two linked key enzymes in the biosynthetic pathway of aspartate family amino acids has been studied.[3] The conversion of aspartate into either the storage amino acid asparagine or aspartate family amino acids may be subject to a coordinated, reciprocal metabolic control, and this biochemical branch point is a part of a larger, coordinated regulatory mechanism of nitrogen and carbon storage and utilization.

References[edit]

  1. ^ Kikuchi Y, Kojima H, Tanaka T (April 1999). "Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli". FEMS Microbiol. Lett. 173 (1): 211–5. PMID 10220897. 
  2. ^ Kochhar S, Kochhar VK, Sane PV (April 1998). "Subunit structure of lysine sensitive aspartate kinase from spinach leaves". Biochem. Mol. Biol. Int. 44 (4): 795–806. PMID 9584993. 
  3. ^ Zhu-Shimoni JX, Galili G (March 1998). "Expression of an arabidopsis aspartate Kinase/Homoserine dehydrogenase gene is metabolically regulated by photosynthesis-related signals but not by nitrogenous compounds". Plant Physiol. 116 (3): 1023–8. doi:10.1104/pp.116.3.1023. PMC 35071. PMID 9501134. 

This article incorporates text from the public domain Pfam and InterPro IPR001048

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.

Amino acid kinase family Provide feedback

This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase EC:2.7.2.4, P00561. Acetylglutamate kinase EC:2.7.2.8, Q07905. Glutamate 5-kinase EC:2.7.2.11, P07005. Uridylate kinase EC:2.7.4.-, P29464. Carbamate kinase EC:2.7.2.2, O96432.

Literature references

  1. Ramon-Maiques S, Marina A, Uriarte M, Fita I, Rubio V; , J Mol Biol 2000;299:463-476.: The 1.5 A resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic Archaeon pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight in PUBMED:10860751 EPMC:10860751


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001048

This entry contains proteins with various specificities and includes the aspartate, glutamate and uridylate kinase families. In prokaryotes and plants the synthesis of the essential amino acids lysine and threonine is predominantly regulated by feed-back inhibition of aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). In Escherichia coli, thrA, metLM, and lysC encode aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively [PUBMED:10220897]. The lysine-sensitive isoenzyme of aspartate kinase from spinach leaves has a subunit composition of 4 large and 4 small subunits [PUBMED:9584993].

In plants although the control of carbon fixation and nitrogen assimilation has been studied in detail, relatively little is known about the regulation of carbon and nitrogen flow into amino acids. The metabolic regulation of expression of an Arabidopsis thaliana aspartate kinase/homoserine dehydrogenase (AK/HSD) gene, which encodes two linked key enzymes in the biosynthetic pathway of aspartate family amino acids has been studied [PUBMED:9501134]. The conversion of aspartate into either the storage amino acid asparagine or aspartate family amino acids may be subject to a coordinated, reciprocal metabolic control, and this biochemical branch point is a part of a larger, coordinated regulatory mechanism of nitrogen and carbon storage and utilization.

Gene Ontology

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Domain organisation

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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 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
(135)
Full
(25691)
Representative proteomes NCBI
(16900)
Meta
(9693)
RP15
(1858)
RP35
(3683)
RP55
(4867)
RP75
(5789)
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Format an alignment

  Seed
(135)
Full
(25691)
Representative proteomes NCBI
(16900)
Meta
(9693)
RP15
(1858)
RP35
(3683)
RP55
(4867)
RP75
(5789)
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
(135)
Full
(25691)
Representative proteomes NCBI
(16900)
Meta
(9693)
RP15
(1858)
RP35
(3683)
RP55
(4867)
RP75
(5789)
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_100 (release 2.1)
Previous IDs: aakinase;
Type: Family
Author: Bateman A, Birney E, Griffiths-Jones SR
Number in seed: 135
Number in full: 25691
Average length of the domain: 240.60 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 64.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.9 24.9
Trusted cut-off 25.0 24.9
Noise cut-off 24.7 24.8
Model length: 242
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Acetyltransf_1 P-II AA_kinase

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 AA_kinase domain has been found. There are 286 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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