Nucleotide Excision Proteins

     Nucleotide Excision Proteins are proteins involved in DNA repair. Nucleotide Excision Repair occurs in Prokaryotes and in Eukaroytes.  In Eukaroytes there are two types of NER: Global Genomic Nucleotide Excision Repair and Transcription Coupled Nucleotide Excision Repair. 

The steps in all Nucleotide Repair

1. Recognize the damaged DNA

2. Proteins bind to the damaged DNA

3. Cut out the damaged DNA

4. Remove damaged DNA

5.  Fill the empty space with the correct and nonmutated DNA nucleotides

6. Ligate the DNA together.

Nucleotide Excision Repair in Prokaryotes:

 The proteins that are involved are Uvr A, Uvr B, Uvr C, Uvr D (also known as DNA Helicase II), DNA Polymerase I, and DNA Ligase  Here is a very good animation of Nucleotide Excision Repair.

Nucleotide Excision Repair in Eukaroytes

 The proteins involved in NER and their functions are listed in the table below. All the proteins in green form a complex called TFIIH which is essential in Nucleotide Excision Repair. 

Steps in Global Genomic NER.

  1.  XPC-HR23B complex binds to the area of distortion in the DNA helix where the damages are located. (Sugasawa et. al. 2001).  This binding causes local undwinding of the DNA.(Mullenders et. al 2001).  XPC-HR23B recruits TFIIH to the damaged site (Yokoi et. al. 2000).   The XPC-HR23B complex is only needed in Global Genome Repair (Mullenders et. al. 2001).

2.  TFIIH is the general transcription factor that binds to the open stranded DNA.  XPB and XPD, are 2 of the 10 subunits that make up TFIIH.  XPB and XPD are helicases and use ATP to unwind the DNA (Nucleotide Excision Repair 2006). XPB unwinds from 3'-5'.  XPD unwinds from 5'-3' (Mullenders et. al 2001). The unwinding makes a bubble 20-30 nucleotides long (Nucleotide Excision Repair 2006).

3.  XPB starts unwinding the DNA which allows XPA protein to bind to the damanged site and then helps recuite other damage reapair proteins (Mullenders et. al 2001). XPA and ensures that the damaged DNA will be removed (Nucleotide Excision Repair 2006).

4. Then RPA (replication protein A) binds with XPA (Mullenders et. al. 2001) .  The RPA is a heterotrimer DNA binding protein that protects both of the separated strands of the DNA in the open complex (Nucleotide Excision Repair 2006).

5. XPG then comes in while XPC-HR23B leave the DNA (Nucleotide Excision Repair 2006).

6. XPF-ERCC1 complex is also recruited to the DNA.  XPG and XPF-ERCC1 are endonucleases.  XPG cuts the DNA at the 3' side while XPF-ERCC1 cuts at the 5' side (Mullenders et. al. 2001).  XPG cuts 2-8 nucleotides away from the damaged site while the XPF-ERCC1 cuts 15-24 nucleotides away (Nucleotide Excision Repair 2006).  The cut ranges from 24-32 nucleotides (Nucleotide Excision Repair 2006).

7. XPA, TFIIH, XPG, and XPF-ERCCQ leave the site while RFC, PCNA and DNA polymerase delta or epsilon fill in the gap starting at the 3'end.(Nucleotide Excision Repair 2006).  Then DNA Ligase I seals the nick.Nucleotide Excision Repair 2006.

The figure shows steps 1-5.  The next Figure shows steps 6 and 7.

 Transcription Coupled Nucleotide Excision Repair

Transcription Coupled Nucleotide Excision Repair process happens during transcription (Nucleotide Excision Repair 2006).   All the proteins above are needed except XPE, XPC, and HR23B (Nucleotide Excision Repair 2006).  The protein that is used to locate the damaged area is RNA polymerase (Nucleotide Excision Repair 2006).  It is thought that RNA polymerase slows down or stops when it runs into damaged site(Nucleotide Excision Repair 2006.)  After the damage has been located CSA and CSB help recruit TFIIH and also displace RNA polymerase.  The rest of the repair is the same as in Global Genome NER in steps 3-8.  This figure shows the first steps of transcription coupled nucleotide excision repair.

 Diseases:

Mutations in the Nucleotide Repair Proteins can results in the following diseases. 

1. Xeroderma Pigmentosum

This disease is caused by a mutation in either the XPA, XPB, XPC, XPD, XPE, XPG, ERCC1 or the Pol H gene, 50% of XP is caused by a mutation of the XPA and XPC gene (Kraemer 2008).  XP is an autosomal recessive disease (Hedera, 2009). Symptoms include severe sensitivity to UV light, abdominal skin pigmentation, neurological problems including mental retardation, spasticity and microcephaly  (Hedera, 2009).Patients with Xeroderma Pigmentosum have a 1000 times greater chance of getting melanoma (Wang et, al. 2009).Diagnosis, testing and managing the disease can be found at this website by Kenneth H Kraemer MD.

2. Cockayne's Syndrome

This is an autosomal recessive disease where the cells are not able to perform transcription coupled Nucleotide Excision Repair (Humpath.com) .  Mutation in the CSA or CSB gene can lead to Cockayne's Syndrome (Humpath.com).  Mutation of the CSA or the ERCC8 gene causes 25% of Cockayne's Syndrome A, while mutation in the  ERCC6 gene cause 75% of Cockayne's Syndrome type B (Neilan 2006).  Mutation of the ERCC6 which is located at the 10q11 encodes for a helicase (Carter et. al. 2007).  The symptoms include sensitivity to sunlight, short stature and the appearance of premature aging (Genes and Disease).  The different types of cockayne's syndrome CSI, CSII, CSIII and Xeroderma Pigmentosum-Cockayne's syndrome (Neilan 2006).  People that have Cockayne's syndrome have an average life span of 12 years (Humpath.com).  For more details about this disease check out the websites below:

1.  http://emedicine.medscape.com/article/942516-overview

2. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=cockayne

3. http://www.humpath.com/spip.php?page=article&id_article=3478

3. Trichothiodystrophy