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45  structures 1425  species 0  interactions 2328  sequences 33  architectures

Family: CKS (PF01111)

Summary: Cyclin-dependent kinase regulatory subunit

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This is the Wikipedia entry entitled "Cyclin-dependent kinase regulatory subunit family". More...

Cyclin-dependent kinase regulatory subunit family Edit Wikipedia article

CKS
PDB 1dks EBI.jpg
ckshs1: human cyclin dependent kinase subunit, type 1 in complex with phosphate
Identifiers
SymbolCKS
PfamPF01111
InterProIPR000789
PROSITEPDOC00728
SCOP21cks / SCOPe / SUPFAM

In molecular biology, the cyclin-dependent kinase regulatory subunit family is a family of proteins consisting of the regulatory subunits of cyclin-dependent protein kinases.

In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division.[1] The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure.[2] Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs.[3] Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation.[2][3]

This family includes the CKS1B and CKS2 genes in mammals.

References

  1. ^ Brizuela L, Draetta G, Beach D (November 1987). "p13suc1 acts in the fission yeast cell division cycle as a component of the p34cdc2 protein kinase". EMBO J. 6 (11): 3507–14. doi:10.1002/j.1460-2075.1987.tb02676.x. PMC 553810. PMID 3322810.
  2. ^ a b Parge HE, Arvai AS, Murtari DJ, Reed SI, Tainer JA (October 1993). "Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control". Science. 262 (5132): 387–95. doi:10.1126/science.8211159. PMID 8211159.
  3. ^ a b Tang Y, Reed SI (May 1993). "The Cdk-associated protein Cks1 functions both in G1 and G2 in Saccharomyces cerevisiae". Genes Dev. 7 (5): 822–32. doi:10.1101/gad.7.5.822. PMID 8491379.
This article incorporates text from the public domain Pfam and InterPro: IPR000789

External links

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000789

In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division [ PUBMED:3322810 ]. The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure [ PUBMED:8211159 ]. Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs [ PUBMED:8491379 ]. Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation [ PUBMED:8491379 , PUBMED:8211159 ].

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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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...

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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
(92)
Full
(2328)
Representative proteomes UniProt
(3886)
RP15
(483)
RP35
(1038)
RP55
(1761)
RP75
(2369)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(92)
Full
(2328)
Representative proteomes UniProt
(3886)
RP15
(483)
RP35
(1038)
RP55
(1761)
RP75
(2369)
Alignment:
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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
(92)
Full
(2328)
Representative proteomes UniProt
(3886)
RP15
(483)
RP35
(1038)
RP55
(1761)
RP75
(2369)
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: Sarah Teichmann
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 92
Number in full: 2328
Average length of the domain: 69.00 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 53.69 %

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 27.0 27.0
Trusted cut-off 27.7 27.2
Noise cut-off 26.6 25.8
Model length: 68
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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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 CKS domain has been found. There are 45 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
A0A1D6H2Z1 View 3D Structure Click here
A0A2R8PV14 View 3D Structure Click here
A2XCH8 View 3D Structure Click here
A4I8J7 View 3D Structure Click here
A8XMF2 View 3D Structure Click here
B0G102 View 3D Structure Click here
B1WC51 View 3D Structure Click here
B2RZ99 View 3D Structure Click here
B4FSK8 View 3D Structure Click here
B6SLG7 View 3D Structure Click here
D3ZGT4 View 3D Structure Click here
F1M990 View 3D Structure Click here
I1LRB4 View 3D Structure Click here
O23249 View 3D Structure Click here
P08463 View 3D Structure Click here
P20486 View 3D Structure Click here
P33552 View 3D Structure Click here
P56390 View 3D Structure Click here
P61024 View 3D Structure Click here
P61025 View 3D Structure Click here
Q0P5A5 View 3D Structure Click here
Q17868 View 3D Structure Click here
Q1LX17 View 3D Structure Click here
Q24152 View 3D Structure Click here
Q2KJI1 View 3D Structure Click here
Q3UNC9 View 3D Structure Click here
Q4CLH8 View 3D Structure Click here
Q4DMY8 View 3D Structure Click here
Q59LQ4 View 3D Structure Click here
Q6DEL8 View 3D Structure Click here
Q6PS57 View 3D Structure Click here
Q6T300 View 3D Structure Click here
Q8I283 View 3D Structure Click here
Q8I2S1 View 3D Structure Click here
Q95XM4 View 3D Structure Click here
Q9SJJ5 View 3D Structure Click here
Q9VHN1 View 3D Structure Click here