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147  structures 6694  species 0  interactions 15422  sequences 149  architectures

Family: PRK (PF00485)

Summary: Phosphoribulokinase / Uridine kinase family

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Phosphoribulokinase / Uridine kinase family Provide feedback

This family matches three types of P-loop containing kinases: phosphoribulokinases [1] uridine kinases [2] and bacterial pantothenate kinases(CoaA) [3]. Arabidopsis and other organisms have a dual uridine kinase/uracil phosphoribosyltransferase protein where the N-terminal region consists of a UK domain and the C-terminal region of a UPRT domain [4].

Literature references

  1. Harrison DH, Runquist JA, Holub A, Miziorko HM; , Biochemistry 1998;37:5074-5085.: The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase. PUBMED:9548738 EPMC:9548738

  2. Neuhard J, Tarpo L;, J Bacteriol. 1993;175:5742-5743.: Location of the udk gene on the physical map of Escherichia coli. PUBMED:8366067 EPMC:8366067

  3. Song WJ, Jackowski S;, J Bacteriol. 1992;174:6411-6417.: Cloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coli. PUBMED:1328157 EPMC:1328157

  4. Islam MR, Kim H, Kang SW, Kim JS, Jeong YM, Hwang HJ, Lee SY, Woo JC, Kim SG;, Plant Mol Biol. 2007;63:465-477.: Functional characterization of a gene encoding a dual domain for uridine kinase and uracil phosphoribosyltransferase in Arabidopsis thaliana. PUBMED:17143579 EPMC:17143579


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006083

Phosphoribulokinase (PRK) EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms [ PUBMED:2175647 ]. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups.

Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP

Pantothenate kinase ( EC ) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP.

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 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 243 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 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 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 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 GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 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 OPA1_C 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 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK 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

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
(9)
Full
(15422)
Representative proteomes UniProt
(54367)
RP15
(2060)
RP35
(7203)
RP55
(14420)
RP75
(23191)
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HTML View             
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
(9)
Full
(15422)
Representative proteomes UniProt
(54367)
RP15
(2060)
RP35
(7203)
RP55
(14420)
RP75
(23191)
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
(9)
Full
(15422)
Representative proteomes UniProt
(54367)
RP15
(2060)
RP35
(7203)
RP55
(14420)
RP75
(23191)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 9
Number in full: 15422
Average length of the domain: 177.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 51.58 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 196
Family (HMM) version: 20
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

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 PRK domain has been found. There are 147 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
A0A0P0W8V3 View 3D Structure Click here
A0A0P0W8V3 View 3D Structure Click here
A0A0R0FQY0 View 3D Structure Click here
A0A0R0JD42 View 3D Structure Click here
A0A0R0JPT3 View 3D Structure Click here
A0A0R4IEL1 View 3D Structure Click here
A0A0R4J5Y3 View 3D Structure Click here
A0A1D6E0T9 View 3D Structure Click here
A0A1D6ESS2 View 3D Structure Click here
A0A1D6HHN9 View 3D Structure Click here
A0A1D6J516 View 3D Structure Click here
A0A1D6KJU1 View 3D Structure Click here
A0A1D6LI73 View 3D Structure Click here
A0A1D6QVF4 View 3D Structure Click here
A0A1D8PQM3 View 3D Structure Click here
A0A1D8PSP6 View 3D Structure Click here
A0A2R8Q5J9 View 3D Structure Click here
A4I754 View 3D Structure Click here
B0S7A4 View 3D Structure Click here
B4FN69 View 3D Structure Click here
B4FQ59 View 3D Structure Click here
B5DF24 View 3D Structure Click here
B8A064 View 3D Structure Click here
C7J1V7 View 3D Structure Click here
D3ZYQ8 View 3D Structure Click here
E9QGS0 View 3D Structure Click here
F4INB5 View 3D Structure Click here
F4INB5 View 3D Structure Click here
H2L2A8 View 3D Structure Click here
I1J4L6 View 3D Structure Click here
I1J693 View 3D Structure Click here
I1JJM2 View 3D Structure Click here
I1KM57 View 3D Structure Click here
I1KM57 View 3D Structure Click here
I1KYV2 View 3D Structure Click here
I1L540 View 3D Structure Click here
I1MLJ3 View 3D Structure Click here
I1MTB0 View 3D Structure Click here
I1MUP0 View 3D Structure Click here
I1N6U6 View 3D Structure Click here
I1N9M3 View 3D Structure Click here
K7K801 View 3D Structure Click here
K7KFC0 View 3D Structure Click here
K7LUR9 View 3D Structure Click here
K7LUU0 View 3D Structure Click here
K7M4A7 View 3D Structure Click here
K7MQF6 View 3D Structure Click here
K7N0S4 View 3D Structure Click here
K7N0S4 View 3D Structure Click here
O65583 View 3D Structure Click here
O74427 View 3D Structure Click here
O94642 View 3D Structure Click here
P0A6I3 View 3D Structure Click here
P0A8F4 View 3D Structure Click here
P0AEX5 View 3D Structure Click here
P25697 View 3D Structure Click here
P27515 View 3D Structure Click here
P52623 View 3D Structure Click here
P53915 View 3D Structure Click here
P9WPA7 View 3D Structure Click here
Q0J0L4 View 3D Structure Click here
Q12084 View 3D Structure Click here
Q17413 View 3D Structure Click here
Q2FXW6 View 3D Structure Click here
Q2QMK2 View 3D Structure Click here
Q53LT4 View 3D Structure Click here
Q54R62 View 3D Structure Click here
Q55EL3 View 3D Structure Click here
Q5A9Z7 View 3D Structure Click here
Q5ANN6 View 3D Structure Click here
Q66I71 View 3D Structure Click here
Q6K7V0 View 3D Structure Click here
Q6YV21 View 3D Structure Click here
Q6Z8F4 View 3D Structure Click here
Q6ZIA3 View 3D Structure Click here
Q7SYM0 View 3D Structure Click here
Q7ZV79 View 3D Structure Click here
Q8MQK4 View 3D Structure Click here
Q8T154 View 3D Structure Click here
Q8VYB2 View 3D Structure Click here
Q91YL3 View 3D Structure Click here
Q944I4 View 3D Structure Click here
Q99PM9 View 3D Structure Click here
Q9BZX2 View 3D Structure Click here
Q9C664 View 3D Structure Click here
Q9C9B9 View 3D Structure Click here
Q9FKS0 View 3D Structure Click here
Q9GNF0 View 3D Structure Click here
Q9HA47 View 3D Structure Click here
Q9LK34 View 3D Structure Click here
Q9LTY6 View 3D Structure Click here
Q9NWZ5 View 3D Structure Click here
Q9QYG8 View 3D Structure Click here
Q9UTC5 View 3D Structure Click here
Q9VC99 View 3D Structure Click here