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76  structures 8075  species 0  interactions 15614  sequences 171  architectures

# Summary: Shikimate kinase

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 "Shikimate kinase". More...

# Shikimate kinase

In enzymology, a shikimate kinase (EC 2.7.1.71) is an enzyme that catalyzes the chemical reaction

ATP + shikimate ${\displaystyle \rightleftharpoons }$ ADP + shikimate 3-phosphate

Thus, the two substrates of this enzyme are ATP and shikimate, whereas its two products are ADP and shikimate 3-phosphate.

This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:shikimate 3-phosphotransferase. Other names in common use include shikimate kinase (phosphorylating), and shikimate kinase II. This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis.

## Structural studies

As of late 2007, 26 structures have been solved for this class of enzymes, with PDB accession codes 1E6C, 1KAG, 1L4U, 1L4Y, 1SHK, 1U8A, 1VIA, 1WE2, 1ZUH, 1ZUI, 1ZYU, 2DFN, 2DFT, 2G1J, 2G1K, 2IYQ, 2IYR, 2IYS, 2IYT, 2IYU, 2IYV, 2IYW, 2IYX, 2IYY, 2IYZ, and 2SHK.

## References

• Morell H, Sprinson DB (1968). "Shikimate kinase isoenzymes in Salmonella typhimurium". J. Biol. Chem. 243: 676â€“7. PMIDÂ 4866525.

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.

# Shikimate kinase

No Pfam abstract.

This tab holds annotation information from the InterPro database.

# InterPro entry IPR031322

Shikimate kinase ( EC ) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) [ PUBMED:7612934 ]. The enzyme catalyses the following reaction:

ATP + shikimate = ADP + shikimate-3-phosphate

The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship [ PUBMED:7703851 ]. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [ PUBMED:9600856 ].

The N terminus of threonine synthase-like 1 from metazoan shares protein sequence similarity with shikimate kinase and is included in this entry. However, their functions may be different.

# Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

# 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
(78)
Full
(15614)
Representative proteomes UniProt
(64798)
RP15
(2021)
RP35
(7219)
RP55
(15118)
RP75
(26185)
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, not generated, not available.

## Format an alignment

Seed
(78)
Full
(15614)
Representative proteomes UniProt
(64798)
RP15
(2021)
RP35
(7219)
RP55
(15118)
RP75
(26185)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(78)
Full
(15614)
Representative proteomes UniProt
(64798)
RP15
(2021)
RP35
(7219)
RP55
(15118)
RP75
(26185)

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.

# 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

 Seed source: Prosite Previous IDs: none Type: Domain Sequence Ontology: SO:0000417 Author: Finn RD , Bateman A Number in seed: 78 Number in full: 15614 Average length of the domain: 154.1 aa Average identity of full alignment: 23 % Average coverage of the sequence by the domain: 47.34 %

## HMM information

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 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 22.0 22.0
Model length: 158
Family (HMM) version: 25

# Species distribution

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### Colour assignments

 Archea Eukaryota Bacteria Other sequences Viruses Unclassified Viroids 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 SKI domain has been found. There are 76 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.

# 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