FANCD2/FANCI-associated nuclease 1 (KIAA1018) is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...

that in

humans Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

is encoded by the FAN1

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

. It is a structure dependent endonuclease and a member of the

myotubularin Myotubularin domain represents a region within eukaryotic myotubularin-related proteins that is sometimes found with the GRAM domain . Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate Phosp ...

-related class 1 cysteine-based

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

tyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the G ...

phosphatases. It is thought to play an important role in the

Fanconi Anemia Fanconi anaemia (FA) is a rare genetic disease resulting in impaired response to DNA damage. Although it is a very rare disorder, study of this and other bone marrow failure syndromes has improved scientific understanding of the mechanisms of no ...

(FA) pathway.

Structure

FAN1 is a protein of 1017 amino acids. Several crystal structures of the residues 373-1017 have been characterized. This portion of FAN1 contains three domains: an SAP domain (primary-DNA binding domain), a TPR domain (mediating interdomain interaction and dimerization interface) and the

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...

-type replication-repair nuclease module (VRR_NUC, catalytic site) (Figure 1). DNA binding promotes dimerization of FAN1 in a "head to tail" fashion. The SAP region contains three major components: α₉, α₅β₁, and α₇. The core helix α₉ stabilizes the protein as it moves through dimer configurations and mediates the interactions between α₅β₁ and α₇ as they adjust their positions. These three configurations are the substrate scanning, substrate latching and substrate unwinding forms (figure 2). In the FAN1 dimer, the SAP regions of both FAN1 enzymes make contact with the DNA duplex (dsDNA). This double contact facilitates DNA induced dimerization, as well as guiding the single stranded (ssDNA) into the SAP domain of the downstream enzyme (^PSAP). The SAP domain of the upstream FAN1 component enzyme (^ASAP) aids in guiding the DNA to ^PSAP. The SAP surface facing the

catalytic Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recyc ...

site is the most conserved region between FAN1 homologs. It is positively charged for favorable hydrogen bonding and electrostatic interactions with DNA. In particular, residues Y374 and Y436 form hydrogen bonds with the phosphate backbone. FAN1 can bind DNA in either direction. However, when the 5' flab is facing away from the VRR_NUC site, substrate latching and unwinding cannot occur. The unresolved portion of FAN1 contains a Zinc finger at the N terminus called a UBZ region. This is present in proteins that bind to

ubiquitin Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...

ated proteins, and is highly conserved across eukaryotes. This Zinc finger is crucial for recruitment to the ubiquitinated FANCD2/FANCI complex, and is found in other nucleases. The VRR_Nuc catalytic domain is located at the C terminus and contains the endonuclease functionality. FAN1 is the first known instance of a virus type replication-repair nuclease module in eukaryotes. It is normally found as a standalone domain in bacterial and viral Holliday Junction Resolvases (HJR). FAN1 does not exhibit any activity on Holliday Junction (HJ) substrates. A subdomain of SAP consisting of six

α helices The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...

connected to the VRR_Nuc region is thought to inhibit HJR activity.

Function

Substrate scanning, latching and unwinding by FAN1

Interstrand

DNA crosslink In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite stra ...

s (ICLs) effectively block the progression of transcription and replication machineries. Release of this block, referred to as unhooking, is thought to require incision of one strand of the duplex on either side of the ICL. Repair of interstrand

s is triggered when the DNA replication fork is unable to continue. The FA proteins play an elaborate role with FAN1 to remove these ICLs. The pathway consists of 15 known proteins. Three of them form the FA AP24-MHF1/2 complex which recognizes the ICL (from stalled replication forks). This recruits the FA core complex, which consists of 8 proteins. This complex monoubiquitinates FANCD2 and FANCI, which allows it to form a heterodimer. It is this complex that recruits FAN1 as well as other nucleases such as SLX4. Ubiquinated FANCD2 interacts with the FAN1 nuclease. Upon its recruitment by FANCD2, FAN1 acts to restrain DNA replication fork progression and to prevent chromosome abnormalities from occurring when DNA replication forks stall. FAN1 is typically localized in the nucleus, but forms very distinct loci at damaged regions when ICLs are present. The FAN1 protein possesses endonuclease and exonuclease functions to remove ICLs. At a replication fork arrested at an ICL, FAN1 nuclease action can catalyze incisions in the double-stranded region. It is thought that this process consists of unhooking the crosslink and separating the DNA strands through two incision events, yielding one strand with a crosslinked nucleotide and another strand with a gap. FAN1 preferentially acts as a 5’ flap endonuclease. This is illustrated in Figure 2, which shows the sequence of substrate scanning, latching, and unwinding. It usually cleaves about 5 nucleotides from a junction. FAN1 will also incise at splayed arms, three way junctions, and 3’ flaps (in order of decreasing preference). In high concentrations FAN1 has been shown to exhibit 3’ 5’ exonuclease activity. In blunt end substrates, FAN1 has also 5’ recessed ends. However, FAN1 does not appear to bind to single stranded DNA. The presence of the FANCD2/FANCI complex is unaffected by knockdown of FAN1. This is because FAN1 acts downstream to the recruitment of FANCD2/FANCI. FAN1 has also been shown to increase the frequency of

homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...

. This suggests that the gapped intermediate that forms following ICL unhooking may be repaired through HR when homologous chromosomes are present. FAN1 does not appear to be involved in other types of

DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA da ...

, as it does not localize to DNA upon

irradiation Irradiation is the process by which an object is exposed to radiation. The exposure can originate from various sources, including natural sources. Most frequently the term refers to ionizing radiation, and to a level of radiation that will serve ...

Clinical significance

Mutations affecting the function of the 15 known FA genes are associated with Fanconi anemia, a recessive autosomal disorder. It is characterized by congenital abnormalities as well as

anemia Anemia or anaemia (British English) is a blood disorder in which the blood has a reduced ability to carry oxygen due to a lower than normal number of red blood cells, or a reduction in the amount of hemoglobin. When anemia comes on slowly, t ...

, bone marrow failure, and

cancer Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal b ...

predisposition in childhood. However, some patients have “unassigned” Fanconi Anemia where no mutations in the known FA genes can be found. Mutations in FAN1 can result in chronic

kidney The kidneys are two reddish-brown bean-shaped organs found in vertebrates. They are located on the left and right in the retroperitoneal space, and in adult humans are about in length. They receive blood from the paired renal arteries; blo ...

diseases and neurological conditions such as

schizophrenia Schizophrenia is a mental disorder characterized by continuous or relapsing episodes of psychosis. Major symptoms include hallucinations (typically hearing voices), delusions, and disorganized thinking. Other symptoms include social wit ...

. However, recent research has called into question the categorization of FAN1 as an FA gene. In 2015 researchers studied four individuals with chromosomal

microdeletion In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is left out during DNA replication. Any number of nucleoti ...

of 15q13.3. Analysis of

blood Blood is a body fluid in the circulatory system of humans and other vertebrates that delivers necessary substances such as nutrients and oxygen to the cells, and transports metabolic waste products away from those same cells. Blood in the cir ...

samples revealed only mild ICL agent sensitivity and chromosomal fragility consistent with Fanconi Anemia. A deficiency of FAN1 increases in vitro sensitivity to cisplatin and mitomycin C, two crosslinking agents FAN1 is also able to repair mitomycin C induced double strand breaks. Germline mutations in the ''FAN1'' gene can cause hereditary colorectal cancer due to defective DNA repair.

Structure

Function

Clinical significance

References

Further reading