Guanine nucleotide exchange factor
Encyclopedia
Guanine nucleotide exchange factors (GEFs) activate monomeric GTPases by stimulating the release of guanosine diphosphate
(GDP) to allow binding of guanosine triphosphate
(GTP). A variety of unrelated structural domains have been shown to exhibit guanine nucleotide exchange activity. Some GEFs can activate multiple GTPases while others are specific to a single GTPase.
and are involved in essential cell processes such as cell differentiation and proliferation, cytoskeletal organization, vesicle trafficking, and nuclear transport. GTPases are active when bound to GTP and inactive when bound to GDP, allowing their activity to be regulated by GEFs and the opposing GTPase activating proteins (GAPs).
GDP disassociates from inactive GTPases very slowly. The binding of GEFs to their GTPase substrates catalyzes the dissociation of GDP, allowing a GTP molecule to bind in its place. GEFs function to promote the dissociation of GDP. After GDP has disassociated from the GTPase, GTP generally binds in its place, as the cytosolic ratio of GTP is much higher than GDP at 10:1. The binding of GTP to the GTPase results in the release of the GEF, which can then activate a new GTPase. Thus, GEFs both destabilize the GTPase interaction with GDP and stabilize the nucleotide free GTPase until a GTP molecule binds to it. GAPs act antagonistically to inactivate GTPases by increasing their intrinsic rate of GTP hydrolysis. GDP remains bound to the inactive GTPase until a GEF binds and stimulates its release.
The localization of GEFs can determine where in the cell a particular GTPase will be active. For example, the Ran
GEF, RCC1
, is present in the nucleus while the Ran GAP is present in the cytosol, modulating nuclear import and export of proteins. RCC1 converts RanGDP to RanGTP in the nucleus, activating Ran for the export of proteins. When the Ran GAP catalyzes conversion of RanGTP to RanGDP in the cytosol, the protein cargo is released.
-binding loop of the GTPase interact with the phosphates of the nucleotide and a coordinating magnesium
ion to maintain high affinity binding of the nucleotide. GEF binding induces conformational changes in the P loop and switch regions of the GTPase while the rest of the structure is largely unchanged. The binding of the GEF sterically hinders the magnesium-binding site and interferes with the phosphate-binding region, while the base-binding region remains accessible. When the GEF binds the GTPase, the phosphate groups are released first and the GEF is displaced upon binding of the entering GTP molecule. Though this general scheme is common among GEFs, the specific interactions between the regions of the GTPase and GEF vary among individual proteins.
, is the catalytic domain of many Ras GEFs, which activate Ras GTPases. The CDC25 domain comprises approximately 500 amino acids and was first identified in the CDC25 protein in budding yeast Saccharomyces cerevisiae
.
s are present in all Dbl family members, which act as GEFs for Rho GTPases. The DH domain, also known as the RhoGEF domain, is responsible for GEF catalytic activity. The PH domain is involved in intracellular targeting of the DH domain. The PH domain is generally thought to modulate membrane binding through interactions with phospholipids, but its function has been shown to vary in different proteins. This PH domain is also present in other proteins beyond RhoGEFs. Together, these two domains constitute the minimum structural unit necessary for the activity of Dbl family proteins. The PH domain is located immediately adjacent to the C terminus of the DH domain. There are approximately 70 identified Dbl RhoGEFs in humans. Many of the mammalian Dbl family proteins are cell-type specific.
is the catalytic domain of the DOCK family of Rho GEFs. The DOCK family is a separate subset of GEFs from the Dbl family and bears no structural or sequence relation to the DH domain. There are 11 identified DOCK family members divided into subfamilies based on their activation of Rac
and Cdc42
. DOCK family members are involved in cell migration, morphogenesis and phagocytosis. The DHR2 domain is approximately 400 amino acids. These proteins also contain a second conserved domain, DHR1, which is approximately 250 amino acids. The DHR1 domain been shown to be involved in the membrane localization of some GEFs.
trafficking. Though ARF GEFs are divergent in their overall sequences, they contain a conserved Sec 7 domain. This 200 amino acid region is homologous to the yeast Sec7p protein.
s in response to upstream signals. GEFs are multi-domain proteins and interact with other proteins inside the cell through these domains. Adaptor proteins can modulate GEF activity by interacting with other domains besides the catalytic domain. For example, SOS
1, the Ras GEF in the MAPK/ERK pathway
, is recruited by the adaptor protein GRB2
in response to EGF receptor activation. The binding of SOS1 to GBR2 localizes it to the plasma membrane, where it can activate the membrane bound Ras
. Other GEFs, such as the Rho
GEF Vav1
, are activated upon phosphorylation in response to upstream signals. Secondary messengers such as cAMP
and calcium
can also play a role in GEF activation.
Crosstalk has also been shown between GEFs and multiple GTPase signaling pathways. For example, SOS contains a Dbl homology domain in addition to its CDC25 catalytic domain. SOS can act as a GEF to activate Rac1
, a RhoGTPase, in addition to its role as a GEF for Ras. SOS is therefore a link between the Ras-Family and Rho-Family GTPase signaling pathways.
therapy due to their role in many signaling pathways, particularly cell proliferation. For example, many cancers are caused by mutations in the MAPK/ERK pathway that lead to uncontrolled growth. The GEF SOS1 activates Ras, whose target is the kinase
Raf. Raf is a proto-oncogene because mutations in this protein have been found in many cancers. The Rho GTPase Vav1, which can be activated by the EGF receptor, has been shown to promote tumor proliferation in pancreatic cancer. GEFs represent possible therapeutic targets as they can potentially play a role in regulating these pathways through their activation of GTPases.
Guanosine diphosphate
Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine....
(GDP) to allow binding of guanosine triphosphate
Guanosine triphosphate
Guanosine-5'-triphosphate is a purine nucleoside triphosphate. It can act as a substrate for the synthesis of RNA during the transcription process...
(GTP). A variety of unrelated structural domains have been shown to exhibit guanine nucleotide exchange activity. Some GEFs can activate multiple GTPases while others are specific to a single GTPase.
Function
Guanine Nucleotide Exchange Factors (GEFs) are proteins involved in the activation of small GTPases. Small GTPases act as molecular switches in intracellular signaling pathways and have many downstream targets. The most well known GTPases comprise the Ras superfamilyRas superfamily
The Ras superfamily is a protein superfamily of small GTPases, which are all related, to a degree, to the Ras protein subfamily .There are more than a hundred proteins in the Ras superfamily...
and are involved in essential cell processes such as cell differentiation and proliferation, cytoskeletal organization, vesicle trafficking, and nuclear transport. GTPases are active when bound to GTP and inactive when bound to GDP, allowing their activity to be regulated by GEFs and the opposing GTPase activating proteins (GAPs).
GDP disassociates from inactive GTPases very slowly. The binding of GEFs to their GTPase substrates catalyzes the dissociation of GDP, allowing a GTP molecule to bind in its place. GEFs function to promote the dissociation of GDP. After GDP has disassociated from the GTPase, GTP generally binds in its place, as the cytosolic ratio of GTP is much higher than GDP at 10:1. The binding of GTP to the GTPase results in the release of the GEF, which can then activate a new GTPase. Thus, GEFs both destabilize the GTPase interaction with GDP and stabilize the nucleotide free GTPase until a GTP molecule binds to it. GAPs act antagonistically to inactivate GTPases by increasing their intrinsic rate of GTP hydrolysis. GDP remains bound to the inactive GTPase until a GEF binds and stimulates its release.
The localization of GEFs can determine where in the cell a particular GTPase will be active. For example, the Ran
Ran
-Organizations:* Rainforest Action Network* Russian Academy of Sciences * The Royal Australian Navy-People:* Nissim of Gerona, Rabbi Nissim ben Reuven...
GEF, RCC1
RCC1
Regulator of chromosome condensation 1, also known as RCC1, is the name for a human gene and protein.RCC1 also functions as a guanine nucleotide exchange factor for Ran GTPase.-Interactions:...
, is present in the nucleus while the Ran GAP is present in the cytosol, modulating nuclear import and export of proteins. RCC1 converts RanGDP to RanGTP in the nucleus, activating Ran for the export of proteins. When the Ran GAP catalyzes conversion of RanGTP to RanGDP in the cytosol, the protein cargo is released.
Mechanism
The mechanism of GTPase activation varies among different GEFs. However, there are some similarities in how different GEFs alter the conformation of the G protein nucleotide-binding site. GTPases contain two loops called switch 1 and switch 2 that are situated on either side of the bound nucleotide. These regions and the phosphatePhosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
-binding loop of the GTPase interact with the phosphates of the nucleotide and a coordinating magnesium
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...
ion to maintain high affinity binding of the nucleotide. GEF binding induces conformational changes in the P loop and switch regions of the GTPase while the rest of the structure is largely unchanged. The binding of the GEF sterically hinders the magnesium-binding site and interferes with the phosphate-binding region, while the base-binding region remains accessible. When the GEF binds the GTPase, the phosphate groups are released first and the GEF is displaced upon binding of the entering GTP molecule. Though this general scheme is common among GEFs, the specific interactions between the regions of the GTPase and GEF vary among individual proteins.
Structure and Specificity
Some GEFs are specific to a single GTPase while others have multiple GTPase substrates. While different subfamilies of Ras superfamily GTPases have a conserved GTP binding domain, this is not the case for GEFs. Different families of GEFs correspond to different Ras subfamilies. The functional domains of these GEF families are not structurally related and do not share sequence homology. These GEF domains appear to be evolutionarily unrelated despite similar function and substrates.CDC25 Domain
The CDC25 homology domain, also called the RasGEF domainRasGEF domain
RasGEF domain is domain found in a family of guanine nucleotide exchange factors for Ras-like small GTPases.Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP...
, is the catalytic domain of many Ras GEFs, which activate Ras GTPases. The CDC25 domain comprises approximately 500 amino acids and was first identified in the CDC25 protein in budding yeast Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
.
DH and PH Domains
The Dbl homology and Pleckstrin homology domainPleckstrin homology domain
Pleckstrin homology domain is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton....
s are present in all Dbl family members, which act as GEFs for Rho GTPases. The DH domain, also known as the RhoGEF domain, is responsible for GEF catalytic activity. The PH domain is involved in intracellular targeting of the DH domain. The PH domain is generally thought to modulate membrane binding through interactions with phospholipids, but its function has been shown to vary in different proteins. This PH domain is also present in other proteins beyond RhoGEFs. Together, these two domains constitute the minimum structural unit necessary for the activity of Dbl family proteins. The PH domain is located immediately adjacent to the C terminus of the DH domain. There are approximately 70 identified Dbl RhoGEFs in humans. Many of the mammalian Dbl family proteins are cell-type specific.
DHR2 Domain
The DHR2 domainDHR2 domain
DHR2 , also known as CZH2 or Docker2, is a protein domain of approximately 450-550 amino acids that is present in the DOCK family of proteins. This domain functions as a guanine nucleotide exchange factor domain for small G proteins of the Rho family...
is the catalytic domain of the DOCK family of Rho GEFs. The DOCK family is a separate subset of GEFs from the Dbl family and bears no structural or sequence relation to the DH domain. There are 11 identified DOCK family members divided into subfamilies based on their activation of Rac
RAC
-Companies:* Rent-A-Center, an American public furniture and electronics rent to own company* Royal Automobile Club, a private club in Pall Mall, London* RAC plc, a breakdown company in the United Kingdom...
and Cdc42
CDC42
Cell division control protein 42 homolog also known as CDC42 is a protein involved in regulation of the cell cycle. In humans, CDC42 is encoded by the CDC42 gene.- Function :...
. DOCK family members are involved in cell migration, morphogenesis and phagocytosis. The DHR2 domain is approximately 400 amino acids. These proteins also contain a second conserved domain, DHR1, which is approximately 250 amino acids. The DHR1 domain been shown to be involved in the membrane localization of some GEFs.
Sec7 Domain
The Sec7 domain is responsible for the GEF catalytic activity in ARF GTPases. ARF proteins function in vesicleVesicle (biology)
A vesicle is a bubble of liquid within another liquid, a supramolecular assembly made up of many different molecules. More technically, a vesicle is a small membrane-enclosed sack that can store or transport substances. Vesicles can form naturally because of the properties of lipid membranes , or...
trafficking. Though ARF GEFs are divergent in their overall sequences, they contain a conserved Sec 7 domain. This 200 amino acid region is homologous to the yeast Sec7p protein.
Regulation
GEFs are often recruited by adaptor proteinAdaptor protein
Signal transducing adaptor proteins are proteins which are accessory to main proteins in a signal transduction pathway. These proteins tend to lack any intrinsic enzymatic activity themselves but instead mediate specific protein–protein interactions that drive the formation of protein complexes...
s in response to upstream signals. GEFs are multi-domain proteins and interact with other proteins inside the cell through these domains. Adaptor proteins can modulate GEF activity by interacting with other domains besides the catalytic domain. For example, SOS
SOS
SOS is the commonly used description for the international Morse code distress signal...
1, the Ras GEF in the MAPK/ERK pathway
MAPK/ERK pathway
The MAPK/ERK pathway is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the DNA in the nucleus of the cell. The signal starts when a growth factor binds to the receptor on the cell surface and ends when the DNA in the nucleus expresses a...
, is recruited by the adaptor protein GRB2
Grb2
Growth factor receptor-bound protein 2 also known as Grb2 is an adaptor protein involved in signal transduction/cell communication. In humans, the GRB2 protein is encoded by the GRB2 gene....
in response to EGF receptor activation. The binding of SOS1 to GBR2 localizes it to the plasma membrane, where it can activate the membrane bound Ras
Ras
Ras is the name given to a family of related proteins found inside cells, including human cells. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells...
. Other GEFs, such as the Rho
Rho
Rho is the 17th letter of the Greek alphabet. In the system of Greek numerals, it has a value of 100. It is derived from Semitic resh "head"...
GEF Vav1
VAV1
Proto-oncogene vav is a protein that in humans is encoded by the VAV1 gene.-Interactions:VAV1 has been shown to interact with Ku70, PLCG1, Lymphocyte cytosolic protein 2, Janus kinase 2, SIAH2, S100B, Abl gene, ARHGDIB, SHB, PIK3R1, PRKCQ, Grb2, MAPK1, Syk, Linker of activated T cells, Cbl gene and...
, are activated upon phosphorylation in response to upstream signals. Secondary messengers such as cAMP
Cyclic adenosine monophosphate
Cyclic adenosine monophosphate is a second messenger important in many biological processes...
and calcium
Calcium
Calcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft gray alkaline earth metal, and is the fifth-most-abundant element by mass in the Earth's crust...
can also play a role in GEF activation.
Crosstalk has also been shown between GEFs and multiple GTPase signaling pathways. For example, SOS contains a Dbl homology domain in addition to its CDC25 catalytic domain. SOS can act as a GEF to activate Rac1
RAC1
Ras-related C3 botulinum toxin substrate 1 also known as Rac1 is a protein that in humans is encoded by the RAC1 gene. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.- Function :Rac1 is...
, a RhoGTPase, in addition to its role as a GEF for Ras. SOS is therefore a link between the Ras-Family and Rho-Family GTPase signaling pathways.
GEFs and Cancer
GEFs are potential target for cancerCancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
therapy due to their role in many signaling pathways, particularly cell proliferation. For example, many cancers are caused by mutations in the MAPK/ERK pathway that lead to uncontrolled growth. The GEF SOS1 activates Ras, whose target is the kinase
Kinase
In chemistry and biochemistry, a kinase is a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates, a process referred to as phosphorylation. Kinases are part of the larger family of phosphotransferases...
Raf. Raf is a proto-oncogene because mutations in this protein have been found in many cancers. The Rho GTPase Vav1, which can be activated by the EGF receptor, has been shown to promote tumor proliferation in pancreatic cancer. GEFs represent possible therapeutic targets as they can potentially play a role in regulating these pathways through their activation of GTPases.
Examples of GEFs
- Son of sevenlessSon of SevenlessIn cell signalling, Son of Sevenless refers to a set of genes encoding guanine nucleotide exchange factors that act on the Ras subfamily of small GTPases.-History and name:...
(SOS1) is an important GEF in the cell growth-regulatory MAPK/ERK pathway. SOS1 binds GBR2 at the plasma membrane after EGF receptor activation. SOS1 activates the small G protein Ras. - eIF-2b is a eukaryotic initiation factor necessary to initiate protein translation. eIF-2b regenerates the GTP-bound form of eIF-2 for an additional cycle in protein synthesis initiation, i.e., its binding to the Met-t-RNA.
- G protein-coupled receptors are trans-membrane receptors that act as GEFs for their cognate G proteins upon binding of a ligand. Ligand binding induces a conformational change that allows the GPCR to activate an associated GTPase.
- RCC1RCC1Regulator of chromosome condensation 1, also known as RCC1, is the name for a human gene and protein.RCC1 also functions as a guanine nucleotide exchange factor for Ran GTPase.-Interactions:...
is the guanine nucletoot change factor for Ran GTPase. It localizes to the nucleus and catalyzes the activation of Ran to allow nuclear export of proteins. - Ras-GRF1Ras-GRF1Ras-GRF1 is a guanine nucleotide exchange factor. Its function is to release guanosine diphosphate, GDP, from the signaling protein RAS, thus increasing the activity of RAS by allowing it to bind to guanosine triphosphate, GTP, returning it to its active state. In this way, Ras-GRF1 has a key role...
- KalirinKalirinKalirin also known as Huntingtin-associated protein-interacting protein , protein duo , or serine/threonine-protein kinase with Dbl- and pleckstrin homology domain is a protein that in humans is encoded by the KALRN gene. Kalirin was first identified in 1997 as a protein interacting with...
See also
- Nucleotide exchange factorNucleotide exchange factorNucleotide exchange factors are proteins that stimulate the exchange of nucleoside diphosphates for nucleoside triphosphates bound to other proteins.-Function:...
- GuanineGuanineGuanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
- Small GTPases
- G proteins