Summary: Phosphoribulokinase / Uridine kinase family
Phosphoribulokinase / Uridine kinase family Provide feedback
In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
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
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
|Similarity to PfamA using HHSearch:||ABC_tran CoaE MobB tRNA_lig_kinase AAA_16 AAA_17 AAA_18 AAA_22 AAA_23 AAA_28 AAA_29 AAA_33|
External 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:
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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|kinase activity (GO:0016301)|
|Biological process||metabolic process (GO:0008152)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||12|
|Number in full:||8151|
|Average length of the domain:||168.80 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||60.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 57 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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