Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran Binding Protein 1 (RanBP1) has guanine nucleotide dissociation inhibitory activity, specific for the GTP form of Ran and also functions to stimulate Ran GTPase activating protein(GAP)-mediated GTP hydrolysis by Ran. RanBP1 contributes to maintaining the gradient of RanGTP across the nuclear envelope high (GDI activity) or the cytoplasmic levels of RanGTP low (GAP cofactor) [].All RanBP1 proteins contain an approx 150 amino acid residue Ran binding domain. Ran BP1 binds directly to RanGTP with high affinity.There are four sites of contact between Ran and the Ran binding domain. One of these involves binding of the C-terminal segment of Ran to a groove on the Ran binding domain that is analogous to the surface utilised in the EVH1-peptide interaction []. Nup358 contains four Ran binding domains. The structure of the first of these is known [].
Small GTPases form an independent superfamily within the larger class ofregulatory GTP hydrolases. This superfamily contains proteins that control avast number of important processes and possess a common, structurallypreserved GTP-binding domain [, ]. Sequence comparisons of small G proteinsfrom various species have revealed that they are conserved in primarystructures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), sixβ-strands (B1-B6) and five polypeptide loops (G1-G5). A structuralcomparison of the GTP- and GDP-bound form, allows one to distinguish twofunctional loop regions: switch I and switch II that surround thegamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop)that connects the B1 strand and the A1 helix is responsible for the binding ofthe phosphate groups. The G3 loop provides residues for Mg(2+) and phosphatebinding and is located at the N terminus of the A2 helix. The G1 and G3 loopsare sequentially similar to Walker A and Walker B boxes that are found inother nucleotide binding motifs. The G2 loop connects the A1 helix and the B2strand and contains a conserved Thr residue responsible for Mg(2+) binding.The guanine base is recognised by the G4 and G5 loops. The consensus sequenceNKXD of the G4 loop contains Lys and Asp residues directly interacting withthe nucleotide. Part of the G5 loop located between B6 and A5 acts as arecognition site for the guanine base [].The small GTPase superfamily can be divided in 8 different families:Arf small GTPases. GTP-binding proteins involved in protein trafficking bymodulating vesicle budding and un-coating within the Golgi apparatusRan small GTPases. GTP-binding proteins involved in nucleocytoplasmictransport. Required for the import of proteins into the nucleus and alsofor RNA exportRab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeletonreorganisationRas small GTPases. GTP-binding proteins involved in signaling pathwaysSar1 small GTPases. Small GTPase component of the coat protein complex II(COPII) which promotes the formation of transport vesicles from theendoplasmic reticulum (ER)Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrialproteins involved in mitochondrial traffickingRoc small GTPases domain. Small GTPase domain always found associated withthe COR domain.Ran (or TC4), is an evolutionary conserved member of the Ras superfamily of small GTPases that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran has been implicated in a large number of processes, including nucleocytoplasmic transport, RNA synthesis, processing and export and cell cycle checkpoint control [, ]. Ran plays a crucial role in both import/export pathways and determines the directionality of nuclear transport. Import receptors (importins) bind their cargos in the cytoplasm where the concentration of RanGTP is low (due to action of RanGAP), and release their cargos in the nucleus where the concentration of RanGTP is high (due to action of RanGEF) [, ]. Export receptors (exportins) respond to RanGTP in the opposite manner. Furthermore, it has been shown that nuclear transport factor 2 (NTF2, ) stimulates efficient nuclear import of a cargo protein. NTF2 binds specifically to RanGDP and to the FXFG repeat containing nucleoporins []. Ran is generally included in the RAS 'superfamily' of small GTP-binding proteins [], but it is only slightly related to the other RAS proteins. It also differs from RAS proteins in that it lacks cysteine residues at its C-terminal and is therefore not subject to prenylation. Instead, Ran has an acidic C terminus. It is, however, similar to RAS family members in requiring a specific guanine nucleotide exchange factor (GEF) and a specific GTPase activating protein (GAP) as stimulators of overall GTPase activity.Ran consists of a core domain that is structurally similar to the GTP-binding domains of other small GTPases but, in addition, Ran has a C-terminal extension consisting of an unstructured linker and a 16 residue α-helix that is located opposite the "Switch I"region in the RanGDP structure []. Three regions of Ran change conformation depending on the nucleotide bound, the Switch I and II regions, which interact with the bound nucleotide, as well as the C-terminal extension. In RanGDP, the C-terminal extension contacts the core of the protein, while in RanGTP, the extension is extending away from the core, most likely due to a steric clash between the switch I region and the linker part of the C-terminal extension. This suggests that the C-terminal extension in RanGDP is crucial for shielding residues in the core domain and preventing the switch regions from adopting a GTP-like form. This prevents binding of transport factors to RanGDP that would otherwise lead to uncoordinated interaction between importin beta-like proteins and cellular factors.
This entry represents a group of RanGTP-binding proteins that contain a conserved RanGTP-binding motif, also called a Ran-binding domain (RBD). They have been implicated in nucleocytoplasmic transport. NUP358 (RanBP2) is localised to the cytoplasmic filaments protruding from the nuclear pore complex (NPC) into the cytoplasm, while RanBP3/Hba1 are localised to the nucleoplasm and Nup2 is localised to the NPC. In general, RanBP1 and other members of this protein family increase, via their conserved RBDs, the rate of RanGAP1-mediated GTP hydrolysis on Ran [].
This SPRY domain is found in Ran binding protein M (RanBPM, also known as RanBP9) and RanBP10. RanBPM and RanBP10 arenon-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. RanBPM is a scaffolding protein important for a variety of cellular processes [, ]. RanBP10 has been shown to function as a cytosolic guanine exchange factor and microtubule regulator [, ]. Both of these proteins contain a SPRY domain, which has been implicated in mediating protein-protein interactions with a variety of targets, including the DEAD-box containing ATP-dependent RNA helicase (DDX-4) [, , ].
This entry includes RanGAP1/2 mostly from plants. They are GTPase activators for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state []. RanGAP1 may have a role in spatial signaling during plant cell division [].
This entry represents the Ran-binding domain found in plant NUP50 protein. NUP50 is a nuclear pore complex component involved in nucleocytoplasmic transport via its interactions with importins and Ran [].
This entry represents a structural domain consisting of a 3-layer α/β/α fold. The β layer is composed of seven β-sheets, and the overall order is: (β-hairpin)-β(3)-α-β(4)-α. Domains with this structure are found in the following protein families:Ran-binding protein Mog1, which interacts with Ran GTPase to stimulate guanine nucleotide release, suggesting Mog1 regulates the nuclear transport functions of Ran [, ].The photosystem II (PSII) oxygen-evolving complex protein PsbP, which is a regulator necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [].
The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The Saccharomyces cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with S. cerevisiae RanBP1 (Yrb1p) for binding to the GTP-bound form of S. cerevisiae Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins [].
This entry represents the Ran-binding domain (RBD) found in RanBP1 from humans and Yrb1 from budding yeasts. RanBP1 and Yrb1 are involved in nuclear import and export. RanBP1 and Yrb1 have been shown to shuttle between the nucleus and cytoplasm and the conserved RBD is necessary and sufficient for the essential function and nucleocytoplasmic shuttling []. RanBP1/Yrb1 acts as a negative regulator of Regulator of chromosome condensation 1 (RCC1) by inhibiting RCC1-stimulated guanine nucleotide release from Ran [].
Segregation of nuclear and cytoplasmic processes facilitates regulation of many eukaryotic cellular functions such as gene expression and cell cycle progression. Trafficking through the nuclear pore requires a number of highly conserved soluble factors that escort macromolecular substrates into and out of the nucleus. The Mog1 protein has been shown to interact with RanGTP, which stimulates guanine nucleotide release, suggesting Mog1 regulates the nuclear transport functions of Ran []. The human homologue of Mog1 is thought to be alternatively spliced.
This entry represents the WPP domain-interacting protein (WIP) family which includes WIP1, 2 and 3 from Arabidopsis. These proteins are specific to plants and required for the localisation and anchorage of Ran GTPase-activating proteins (RanGAP) to the nuclear envelope (NE) mediated by WIT1 and WIT2 in undifferentiated cells of root tips [, ]. They are part of the SUN-WIP-WIT2-KAKU1 complex, in which they mediate the transfer of cytoplasmic forces to the nuclear envelope (NE), leading to nuclear shape changes [].
STKs (serine/threonine-protein kinases) catalyse the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek9, also called Nercc1, is primarily a cytoplasmic protein but can also localize in the nucleus. It is involved in modulating chromosome alignment and splitting during mitosis. It interacts with the gamma-tubulin ring complex and the Ran GTPase, and is implicated in microtubule organization []. Nek9 associates with FACT (FAcilitates Chromatin Transcription) and modulates interphase progression []. It also interacts with Nek6, and Nek7, during mitosis, resulting in their activation. Nek9 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control [, ].
Exportins bind cargo molecules in the nuclei and transport them through nuclear pores to the cytoplasm, a process that requires RanGTP. This entry includes Exportin 4 and 7 (also known as RanBP16), proteins that mediate the nuclear export of proteins with broad substrate specificity. They bind cooperatively to its cargo and to the GTPase Ran in its active GTP-bound form. Exportin 4 transports the eukaryotic translation initiation factor 5A (eIF-5A) and Smad3, controlling protein synthesis and Smad signalling [, ].This entry also includes Ran-binding protein 17 from humans.
GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus.Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily [].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry representsthe zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP [].
Ran () is an evolutionary conserved member of the Ras superfamily of small GTPases that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Import receptors bind their cargos in the cytoplasm where the concentration of RanGTP is low and release their cargos in the nucleus where the concentration of RanGTP is high []. Export receptors respond to Ran GTP in the oppositemanner. Nuclear transport factor 2 (NTF2) is a homodimer of approximately 14kDa subunits which stimulates efficient nuclear import of a cargo protein. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. NTF2 binds to RanGDP sufficiently strongly for the complex to remain intact during transport through NPCs, but the interaction between NTF2 and FxFG nucleoporins is much more transient, which would enable NTF2 to move through the NPC by hopping from one repeat to another [, ].NTF2 folds into a cone with a deep hydrophobic cavity, the opening of which is surrounded by several negatively charged residues. RanGDP binds to NTF2 by inserting a conserved phenylalanine residue into the hydrophobic pocket of NTF2 and making electrostatic interactions with the conserved negatively charged residues that surround the cavity.This entry contains predominantly eukaryotic proteins. The following proteins contain a region similar to NTF2:Eukaryotic NXF proteins []. These are nuclear mRNA export factors. These proteins contain, in addition to a NTF2 domain, a number of leucine-rich repeats and a UBA domain.Eukaryotic NXT1/NXT2 proteins []. These proteins are stimulators of protein export for NES-containing proteins. The also play a role in mRNA nuclear export. They heterodimerize with NFX proteins. In contrast to NTF2, NXT1 and NXT2 preferentially bind RanGTP.Eukaryotic Ras-GTPase-activating protein (GAP)-binding proteins (G3BP's). These proteins contain one NTF2 domain and one RRM (see ).
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain superfamily found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP [].
The regulator of chromosome condensation (RCC1) []is a eukaryotic proteinwhich binds to chromatin and interacts with ran, a nuclear GTP-bindingprotein , to promote the loss of bound GDP and the uptake offresh GTP, thus acting as a guanine-nucleotide dissociation stimulator (GDS).The interaction of RCC1 with ran probably plays an important role in theregulation of gene expression.RCC1, known as PRP20 or SRM1 in yeast, pim1 in fission yeast and BJ1 inDrosophila, is a protein that contains seven tandem repeats of a domain ofabout 50 to 60 amino acids. As shown in the following schematicrepresentation, the repeats make up the major part of the length of theprotein. Outside the repeat region, there is just a small N-terminal domain ofabout 40 to 50 residues and, in the Drosophila protein only, a C-terminaldomain of about 130 residues.+----+-------+-------+-------+-------+-------+-------+-------+-------------+|N-t.|Rpt. 1 |Rpt. 2 |Rpt. 3 |Rpt. 4 |Rpt. 5 |Rpt. 6 |Rpt. 7 | C-terminal |+----+-------+-------+-------+-------+-------+-------+-------+-------------+The RCC1-type of repeat is also found in the X-linked retinitis pigmentosaGTPase regulator []. The RCC repeats form a β-propellerstructure.
Ran GTPase is a ubiquitous protein required for nuclear transport, spindle assembly, nuclear assembly and mitotic cell cycle regulation. RanGTPase activating protein 1 (RanGAP1) is one of several RanGTPase accessory proteins. During interphase, RanGAP1 is located in the cytoplasm, while during mitosis it becomes associated with the kinetochores []. Cytoplasmic RanGAP1 is required for RanGTPase-directed nuclear transport. The activity of RanGAP1 requires the accessory protein RanBP1. RanBP1 facilitates RanGAP1 hydrolysis of Ran-GTP, both directly and by promoting the dissociation of Ran-GTP from transport receptors, which would otherwise block RanGAP1-mediated hydrolysis. RanGAP1 is thought to bind to the Switch 1 and Switch 2 regions of RanGTPase. The Switch 2 region can be buried in complexes with karyopherin-beta2, and requires the interaction with RanBP1 to permit RanGAP1 function. RanGAP1 can undergo SUMO (small ubiquitin-like modifier) modification, which targets RanGAP1 to RanBP2/Nup358 in the nuclear pore complex, and is required for association with the nuclear pore complex and for nuclear transport []. The enzymes involved in SUMO modification are located on the filaments of the nuclear pore complex.The RanGAP1 N-terminal domain is fairly well conserved between vertebrate and fungal proteins, but yeast does not contain the C-terminal domain. The C-terminal domain is SUMO-modified and required for the localisation of RanGAP1 at the nuclear pore complex. The structure of the C-terminal domain is multihelical, consisting of two curved alpha/alpha layers in a right-handed superhelix.
Ran GTPase is a ubiquitous protein required for nuclear transport, spindle assembly, nuclear assembly and mitotic cell cycle regulation. RanGTPase activating protein 1 (RanGAP1) is one of several RanGTPase accessory proteins. During interphase, RanGAP1 is located in the cytoplasm, while during mitosis it becomes associated with the kinetochores []. Cytoplasmic RanGAP1 is required for RanGTPase-directed nuclear transport. The activity of RanGAP1 requires the accessory protein RanBP1. RanBP1 facilitates RanGAP1 hydrolysis of Ran-GTP, both directly and by promoting the dissociation of Ran-GTP from transport receptors, which would otherwise block RanGAP1-mediated hydrolysis. RanGAP1 is thought to bind to the Switch 1 and Switch 2 regions of RanGTPase. The Switch 2 region can be buried in complexes with karyopherin-beta2, and requires the interaction with RanBP1 to permit RanGAP1 function. RanGAP1 can undergo SUMO (small ubiquitin-like modifier) modification, which targets RanGAP1 to RanBP2/Nup358 in the nuclear pore complex, and is required for association with the nuclear pore complex and for nuclear transport []. The enzymes involved in SUMO modification are located on the filaments of the nuclear pore complex.The RanGAP1 N-terminal domain is fairly well conserved between vertebrate and fungal proteins, but yeast does not contain the C-terminal domain. The C-terminal domain is SUMO-modified and required for the localisation of RanGAP1 at the nuclear pore complex. The structure of the C-terminal domain is multihelical, consisting of two curved alpha/alpha layers in a right-handed superhelix.
This entry represents a domain found in Nup2, 50 and 61, which are components of the nuclear pore complex. Nucleoporin 50kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha []. NUP2 encodes a non-essential nuclear pore protein that has a central domain similar to those of Nsp1 and Nup1[, ]. Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope [, , ]. The structure of the vertebrate NPC has been studied extensively; recent reviews include [, , , ]. The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate [, ]. Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches [, , , ]. nup2 mutants show genetic interactions with nsp1 and nup1 conditional alleles [, ]. Nup1 interacts with the nuclear import factor Srp1 []and with the small GTPase Ran (encoded by GSP1) [].
GTPases bind to guanosine triphosphate (GTP), hydrolyze gamma-phosphate,release guanosine diphosphate (GDP) and then rebind GTP, a process termed'GTPase cycling'. GTPases are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). The Ras superfamily of small GTPases consists of five subgroups (Ras, Rho, Rab, Ran and Arf) that act as molecular switches in broad and diverse cellular pathways and processes. The Ras superfamily members contain five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases by definition would consist of a GTPase fold lacking one or more of these G motifs [].The p190RhoGAP proteins, p190RhoGAP-A (ARHGAP35) andp190RhoGAP-B (ARHGAP5), are key regulators of Rho GTP hydrolysis and arehighly important for maintenance of proper Rho signaling. They share a domainorganization containing a GTP-binding GTPase domain, four FF domains, twoGTPase-like folds (pG1 and pG2) and a C-terminal GAP domain. Their pG1 (pseudoGTPase1) and pG2 (pseudoGTPase2) domains lack conserved GTPase motifs and don't have nucleotide-binding activity []. This entry represents the pG2 domain.
GTPases bind to guanosine triphosphate (GTP), hydrolyze gamma-phosphate,release guanosine diphosphate (GDP) and then rebind GTP, a process termed'GTPase cycling'. GTPases are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). The Ras superfamily of small GTPases consists of five subgroups (Ras, Rho, Rab, Ran and Arf) that act as molecular switches in broad and diverse cellular pathways and processes. The Ras superfamily members contain five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases by definition would consist of a GTPase fold lacking one or more of these G motifs [].The p190RhoGAP proteins, p190RhoGAP-A (ARHGAP35) andp190RhoGAP-B (ARHGAP5), are key regulators of Rho GTP hydrolysis and arehighly important for maintenance of proper Rho signaling. They share a domainorganization containing a GTP-binding GTPase domain, four FF domains, twoGTPase-like folds (pG1 and pG2) and a C-terminal GAP domain. Their pG1 (pseudoGTPase1) and pG2 (pseudoGTPase2) domains lack conserved GTPase motifs and don't have nucleotide-binding activity []. This entry represents the pG1 domain.
This entry represents the N-terminal domain of importin-beta (also known as karyopherins-beta) that is important for the binding of the Ran GTPase protein [].Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport.Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well.
The 33-residue LIS1 homology (LisH) motif () is found in eukaryotic intracellularproteins involved in microtubule dynamics, cell migration, nucleokinesis andchromosome segregation. The LisH motif is likely to possess a conservedprotein-binding function and it has been proposed that LisH motifs contributeto the regulation of microtubule dynamics, either by mediating dimerization,or else by binding cytoplasmic dynein heavy chain or microtubules directly.The LisH motif is found associated to other domains, such as WD-40 (see), SPRY, Kelch, AAA ATPase, RasGEF, or HEAT (see )[, , ].The secondary structure of the LisH domain is predicted to be two alpha-helices [].Some proteins known to contain a LisH motif are listed below:Animal LIS1. It regulates cytoplasmic dynein function. In Homo sapiens (human) childrenwith defects in LIS1 suffer from Miller-Dieker lissencephaly, a brainmalformation that results in severe retardation, epilepsy and an earlydeath.Emericella nidulans (Aspergillus nidulans) nuclear migration protein nudF, the orthologue of LIS1.Eukaryotic RanBPM, a Ran binding protein involved in microtubulenucleation.Eukaryotic Nopp140, a nucleolar phosphoprotein.Mammalian treacle, a nucleolar protein. In human, defects in treacle arethe cause of Treacher Collins syndrome (TCS), an autosomal dominantdisorder of craniofacial development.Animal muskelin. It acts as a mediator of cell spreading and cytoskeletalresponses to the extracellular matrix component thrombospondin 1.Animal transducin beta-like 1 protein (TBL1).Plant tonneau.Arabidopsis thaliana LEUNIG, a putative transcriptional corepressor thatregulates AGAMOUS expression during flower development.Fungal aimless RasGEF.Leishmania major katanin-like protein.The C-terminal to LisH (CTLH) motif is a predicted α-helical sequence ofunknown function that is found adjacent to the LisH motif in a number of theseproteins but is absent in other (e.g. LIS1) [, , ]. The CTLH domain can alsobe found in the absence of the LisH motif, like in:Arabidopsis thaliana (Mouse-ear cress) hypothetical protein MUD21.5.Saccharomyces cerevisiae yeast protein RMD5.
This is the B30.2/SPRY domain found in Ran binding proteins (RanBPs), such as RanBP M homologue (AtRanBPM) from Arabidopsis [], vacuolar import and degradation protein 30 (Vid30) from Saccharomyces cerevisiae and dual specificity protein kinase splA (SPLA) from Dictyostelium discoideum.The B30.2 domain was first identified as a protein domain encoded by an exon (named B30-2) in the Homo sapiens class I major histocompatibility complex region [], whereas the SPRY domain was first identified in a Dictyostelium discoideum kinase splA and mammalian calcium-release channels ryanodine receptors []. B30.2 domain consists of PRY and SPRY subdomains. The SPRY domains (after SPla and the RYanodine Receptor) are shorter at the N terminus than the B30.2 domains. The ~200-residue B30.2/SPRY (for B30.2 and/or SPRY) domain is present in a large number of proteins with diverse individual functions in different biological processes. The B30.2/SPRY domain in these proteins is likely to function through protein-protein interaction [].The N-terminal ~60 residues of B30.2/SPRY domains are poorly conserved and, as a consequence, a new domain name PRY was coined for a group of similar sequence segments N-terminal to the SPRY domains []. The B30.2/SPRY domain contains three highly conserved motifs (LDP, WEVE and LDYE) []. The B30.2/SPRY domain adopts a highly distorted, compact β-sandwich fold with two additional short beta helices at the N terminus. The beta sandwich of the B30.2/SPRY domain consists of two layers of beta sheets: sheet A composed of eight strands and sheet B composed of seven strands. All the beta strands are in antiparallel arrangement []. The 5th β-strand corresponding to WEVE motif []. Both the N- and C-terminal ends of the B30.2/SPRY domains in general are close to each other [].
