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20  structures 312  species 2  interactions 488  sequences 6  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
Symbol CKS
Pfam PF01111
InterPro IPR000789
PROSITE PDOC00728
SCOP 1cks
SUPERFAMILY 1cks

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[edit]

  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. 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

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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

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Domain organisation

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Alignments

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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.

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(33)
Full
(488)
Representative proteomes NCBI
(442)
Meta
(1)
RP15
(119)
RP35
(178)
RP55
(263)
RP75
(323)
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Format an alignment

  Seed
(33)
Full
(488)
Representative proteomes NCBI
(442)
Meta
(1)
RP15
(119)
RP35
(178)
RP55
(263)
RP75
(323)
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
(33)
Full
(488)
Representative proteomes NCBI
(442)
Meta
(1)
RP15
(119)
RP35
(178)
RP55
(263)
RP75
(323)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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.

Curation View help on the curation process

Seed source: Sarah Teichmann
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 33
Number in full: 488
Average length of the domain: 71.50 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 58.47 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 21.9 22.2
Noise cut-off 18.1 20.1
Model length: 70
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

CKS Pkinase

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 20 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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