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76  structures 8075  species 0  interactions 15614  sequences 171  architectures

Family: SKI (PF01202)

Summary: Shikimate kinase

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This is the Wikipedia entry entitled "Shikimate kinase". More...

Shikimate kinase Edit Wikipedia article

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

ATP + shikimate 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.


Template:Enzyme references

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

External links

The CAS registry number for this enzyme class is Template:CAS registry.

Template:Enzyme links

Gene Ontology (GO) codes

Template:GO code links

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.

Shikimate kinase Provide feedback

No Pfam abstract.

Internal database links

External database links

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...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 245 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR BrxC_BrxD BrxL_ATPase Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot


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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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

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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.

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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 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 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
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


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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.

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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
A0A077Z2S3 View 3D Structure Click here
A0A0D2DMI9 View 3D Structure Click here
A0A0D2FBH4 View 3D Structure Click here
A0A0D2GNU3 View 3D Structure Click here
A0A0H3GK99 View 3D Structure Click here
A0A0H3GYI1 View 3D Structure Click here
A0A0H3GZE8 View 3D Structure Click here
A0A0K0EHC9 View 3D Structure Click here
A0A0N4UQG9 View 3D Structure Click here
A0A0P0WRJ9 View 3D Structure Click here
A0A0R0F8S5 View 3D Structure Click here
A0A0R0IZ75 View 3D Structure Click here
A0A0R0JH37 View 3D Structure Click here
A0A0R0L553 View 3D Structure Click here
A0A175VQK6 View 3D Structure Click here
A0A175W9H9 View 3D Structure Click here
A0A175WJI8 View 3D Structure Click here
A0A1C1CEP6 View 3D Structure Click here
A0A1C1CXW8 View 3D Structure Click here
A0A1D6DWX6 View 3D Structure Click here
A0A1D6HKK5 View 3D Structure Click here
A0A1D6K9Y9 View 3D Structure Click here
A0A1D6KDZ4 View 3D Structure Click here
A0A3Q0KCW4 View 3D Structure Click here
A0KN29 View 3D Structure Click here
A0LUH0 View 3D Structure Click here
A1BER1 View 3D Structure Click here
A1CP85 View 3D Structure Click here
A1D244 View 3D Structure Click here
A1SB14 View 3D Structure Click here
A1SRB6 View 3D Structure Click here
A1TKW2 View 3D Structure Click here
A1WZB0 View 3D Structure Click here
A3LSZ2 View 3D Structure Click here
A3MYR6 View 3D Structure Click here
A3Q9D7 View 3D Structure Click here
A4FBE7 View 3D Structure Click here
A4RD09 View 3D Structure Click here
A4SFH8 View 3D Structure Click here
A4VTX6 View 3D Structure Click here