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4  structures 300  species 3  interactions 702  sequences 19  architectures

Family: Ku_N (PF03731)

Summary: Ku70/Ku80 N-terminal alpha/beta domain

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This is the Wikipedia entry entitled "Ku (protein)". More...

Ku (protein) Edit Wikipedia article

X-ray repair
cross-complementing 5
Ku bound to DNA.png
Crystal structure of human Ku bound to DNA. Ku70 is shown in purple, Ku80 in blue, and the DNA strand in green.[1]
Identifiers
Symbol XRCC5
Alt. symbols Ku80
Entrez 7520
HUGO 12833
OMIM 194364
PDB 1JEY (RCSB PDB PDBe PDBj)
RefSeq NM_021141
UniProt P13010
Other data
Locus Chr. 2 q35
X-ray repair
cross-complementing 6
Identifiers
Symbol XRCC6
Alt. symbols Ku70, G22P1
Entrez 2547
HUGO 4055
OMIM 152690
PDB 1JEY (RCSB PDB PDBe PDBj)
RefSeq NM_001469
UniProt P12956
Other data
Locus Chr. 22 q11-q13
Ku70/Ku80 N-terminal alpha/beta domain
PDB 1jeq EBI.jpg
crystal structure of the ku heterodimer
Identifiers
Symbol Ku_N
Pfam PF03731
Pfam clan CL0128
InterPro IPR005161
SCOP 1jey
SUPERFAMILY 1jey
Ku70/Ku80 beta-barrel domain
PDB 1jey EBI.jpg
crystal structure of the ku heterodimer bound to dna
Identifiers
Symbol Ku
Pfam PF02735
InterPro IPR006164
PROSITE PDOC00252
SCOP 1jey
SUPERFAMILY 1jey
Ku70/Ku80 C-terminal arm
PDB 1jey EBI.jpg
crystal structure of the ku heterodimer bound to dna
Identifiers
Symbol Ku_C
Pfam PF03730
InterPro IPR005160
SCOP 1jey
SUPERFAMILY 1jey
Ku C terminal domain like
PDB 1q2z EBI.jpg
the 3d solution structure of the c-terminal region of ku86
Identifiers
Symbol Ku_PK_bind
Pfam PF08785
InterPro IPR014893
SCOP 1q2z
SUPERFAMILY 1q2z

Ku is a protein that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to human. The ancestral bacterial Ku is a homodimer (two copies of the same protein bound to each other).[2] Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end.[1] Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK.[3] Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind.

Both subunits of Ku have been experimentally knocked out in mice. These mice exhibit chromosomal instability, indicating that NHEJ is important for genome maintenance.[4][5]

In many organisms, Ku has additional functions at telomeres in addition to its role in DNA repair.[6]

Abundance of Ku80 seems to be related to species longevity.[7]

The Ku70 and Ku80 proteins consist of three structural domains. The N-terminal domain is an alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.[8] The central domain of Ku70 and Ku80 is a DNA-binding beta-barrel domain. Ku makes only a few contacts with the sugar-phosphate backbone, and none with the DNA bases, but it fits sterically to major and minor groove contours forming a ring that encircles duplex DNA, cradling two full turns of the DNA molecule. By forming a bridge between the broken DNA ends, Ku acts to structurally support and align the DNA ends, to protect them from degradation, and to prevent promiscuous binding to unbroken DNA. Ku effectively aligns the DNA, while still allowing access of polymerases, nucleases and ligases to the broken DNA ends to promote end joining.[9] The C-terminal arm is an alpha helical region which embraces the central beta-barrel domain of the opposite subunit.[1] In some cases a fourth domain is present at the C-terminus, which binds to DNA-dependent protein kinase catalytic subunit.[10]

References[edit]

  1. ^ a b c PDB 1JEY; Walker JR, Corpina RA, Goldberg J (August 2001). "Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair". Nature 412 (6847): 607–14. doi:10.1038/35088000. PMID 11493912. 
  2. ^ Doherty AJ, Jackson SP, Weller GR (July 2001). "Identification of bacterial homologues of the Ku DNA repair proteins". FEBS Lett. 500 (3): 186–8. doi:10.1016/S0014-5793(01)02589-3. PMID 11445083. 
  3. ^ Carter T, Vancurová I, Sun I, Lou W, DeLeon S (December 1990). "A DNA-activated protein kinase from HeLa cell nuclei". Mol. Cell. Biol. 10 (12): 6460–71. PMC 362923. PMID 2247066. 
  4. ^ Difilippantonio MJ, Zhu J, Chen HT, Meffre E, Nussenzweig MC, Max EE, Ried T, Nussenzweig A (March 2000). "DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation". Nature 404 (6777): 510–4. doi:10.1038/35006670. PMID 10761921. 
  5. ^ Ferguson DO, Sekiguchi JM, Chang S, Frank KM, Gao Y, DePinho RA, Alt FW (June 2000). "The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations". Proc. Natl. Acad. Sci. U.S.A. 97 (12): 6630–3. doi:10.1073/pnas.110152897. PMC 18682. PMID 10823907. 
  6. ^ Boulton SJ, Jackson SP (March 1998). "Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing". EMBO J. 17 (6): 1819–28. doi:10.1093/emboj/17.6.1819. PMC 1170529. PMID 9501103. 
  7. ^ Lorenzini A, Johnson FB, Oliver A, Tresini M, Smith JS, Hdeib M, Sell C, Cristofalo VJ, Stamato TD (Nov–Dec 2009). "Significant Correlation of Species Longevity with DNA Double Strand Break-Recognition but not with Telomere Length". Mech Ageing Dev. 130 (11–12): 784–92. doi:10.1016/j.mad.2009.10.004. PMC 2799038. PMID 19896964. 
  8. ^ Sugihara T, Wadhwa R, Kaul SC, Mitsui Y (April 1999). "A novel testis-specific metallothionein-like protein, tesmin, is an early marker of male germ cell differentiation". Genomics 57 (1): 130–6. doi:10.1006/geno.1999.5756. PMID 10191092. 
  9. ^ Aravind L, Koonin EV (August 2001). "Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system". Genome Res. 11 (8): 1365–74. doi:10.1101/gr.181001. PMC 311082. PMID 11483577. 
  10. ^ Harris R, Esposito D, Sankar A, Maman JD, Hinks JA, Pearl LH, Driscoll PC (January 2004). "The 3D solution structure of the C-terminal region of Ku86 (Ku86CTR)". J. Mol. Biol. 335 (2): 573–82. doi:10.1016/j.jmb.2003.10.047. PMID 14672664. 

This article incorporates text from the public domain Pfam and InterPro IPR005161

This article incorporates text from the public domain Pfam and InterPro IPR006164

This article incorporates text from the public domain Pfam and InterPro IPR005160

This article incorporates text from the public domain Pfam and InterPro IPR014893

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.

Ku70/Ku80 N-terminal alpha/beta domain Provide feedback

The Ku heterodimer (composed of Ku70 P12956 and Ku80 P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].

Literature references

  1. Walker JR, Corpina RA, Goldberg J; , Nature 2001;412:607-614.: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. PUBMED:11493912 EPMC:11493912

  2. Aravind L, Koonin EV; , Genome Res 2001;11:1365-1374.: Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. PUBMED:11483577 EPMC:11483577


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005161

The Ku heterodimer (composed of Ku70 SWISSPROT and Ku80 SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the N-terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [PUBMED:10191092].

Domain organisation

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Pfam Clan

Alignments

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(17)
Full
(702)
Representative proteomes NCBI
(710)
Meta
(4)
RP15
(128)
RP35
(216)
RP55
(324)
RP75
(399)
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  Seed
(17)
Full
(702)
Representative proteomes NCBI
(710)
Meta
(4)
RP15
(128)
RP35
(216)
RP55
(324)
RP75
(399)
Alignment:
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  Seed
(17)
Full
(702)
Representative proteomes NCBI
(710)
Meta
(4)
RP15
(128)
RP35
(216)
RP55
(324)
RP75
(399)
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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:

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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

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Seed source: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 17
Number in full: 702
Average length of the domain: 208.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 32.63 %

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 20.6 20.6
Trusted cut-off 20.7 21.0
Noise cut-off 20.3 20.4
Model length: 224
Family (HMM) version: 10
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Species distribution

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Interactions

There are 3 interactions for this family. More...

Ku_C SAP Ku

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 Ku_N domain has been found. There are 4 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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