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42-443: FtsK is a transmembrane protein composed of three domains: FtsK N , FtsK L , and FtsK C . FtsK functions to coordinate cell division and chromosome segregation through its N-terminal and C-terminal domains. The FtsK N domain is embedded in the cytoplasmic membrane by four transmembrane α-helices. The FtsK L domain extends from the membrane into the cytoplasm. This linking domain varies in length across many bacteria. Found at

84-465: A ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that can be propagated through the assembly in order to act upon a target substrate, either translocating or remodelling the substrate. The central pore may be involved in substrate processing. In the hexameric configuration, the ATP-binding site

126-496: A signal-anchor sequence, with type II being targeted to the ER lumen with its C-terminal domain, while type III have their N-terminal domains targeted to the ER lumen. Type IV is subdivided into IV-A, with their N-terminal domains targeted to the cytosol and IV-B, with an N-terminal domain targeted to the lumen. The implications for the division in the four types are especially manifest at the time of translocation and ER-bound translation, when

168-420: Is a AAA-type ATPase involved in this MVB sorting pathway. It had originally been identified as a ”class E” vps (vacuolar protein sorting) mutant and was subsequently shown to catalyse the dissociation of ESCRT complexes. Vps4p is anchored via Vps46p to the endosomal membrane. Vps4p assembly is assisted by the conserved Vta1p protein, which regulates its oligomerization status and ATPase activity. AAA proteases use

210-575: Is a type of integral membrane protein that spans the entirety of the cell membrane . Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them ( beta-barrels ) can be also extracted using denaturing agents . The peptide sequence that spans

252-453: Is affected. AAA proteins are involved in protein degradation , membrane fusion , DNA replication , microtubule dynamics, intracellular transport, transcriptional activation, protein refolding, disassembly of protein complexes and protein aggregates . Dyneins , one of the three major classes of motor protein , are AAA proteins which couple their ATPase activity to molecular motion along microtubules . The AAA-type ATPase Cdc48p/p97

294-519: Is also a very efficient one. During bacterial replication, in the presence of a dimer the XerCD mechanism is introduced to divide the dimer into two monomers. FtsK is responsible for the activity of the Xer recombination reaction. Specifically, FtsK c is summoned if a chromosome dimer is present at the mid-cell point. The Xer mechanism is activated by overexpression of FtsK, therefore it appears that FtsK activates

336-486: Is also the site of Xer mediated segregation. Translocation of the FtsK C hexamer stops when it reaches the location of the Xer recombinase complex that is associated with the dif site.   Guanosine rich areas of DNA, which are found at the ends of the dif region, are the sites of translocation initiation. These sites are referred to as KOPS motifs. Upon binding a KOPS motif, the FtsK hexamer forms and proceeds towards

378-654: Is found in most bacteria including E. coli , Staphyloccus , and Streptomycetes and in certain Archaea, where the phylogenetic tree is similar to that of bacteria. FtsK family proteins have divergent branch lengths, making it difficult to provide an exact evolutionary timeline. The phylogeny of FtsK can therefore be compared to the time that protein groups VirB4/VirD4 diversified, and slightly earlier than TraB and TcpA as they only occur in Actinomycetota and Bacillota . Transmembrane protein A transmembrane protein

420-529: Is perhaps the best-studied AAA protein. Misfolded secretory proteins are exported from the endoplasmic reticulum (ER) and degraded by the ER-associated degradation pathway ( ERAD ). Nonfunctional membrane and luminal proteins are extracted from the ER and degraded in the cytosol by proteasomes. Substrate retrotranslocation and extraction is assisted by the Cdc48p(Ufd1p/Npl4p) complex on the cytosolic side of

462-687: Is positioned at the interface between the subunits. Upon ATP binding and hydrolysis, AAA enzymes undergo conformational changes in the AAA-domains as well as in the N-domains. These motions can be transmitted to substrate protein. ATP hydrolysis by AAA ATPases is proposed to involve nucleophilic attack on the ATP gamma-phosphate by an activated water molecule, leading to movement of the N-terminal and C-terminal AAA subdomains relative to each other. This movement allows

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504-429: Is technically difficult. There are relatively few examples of the successful refolding experiments, as for bacteriorhodopsin . In vivo , all such proteins are normally folded co-translationally within the large transmembrane translocon . The translocon channel provides a highly heterogeneous environment for the nascent transmembrane α-helices. A relatively polar amphiphilic α-helix can adopt a transmembrane orientation in

546-400: Is thought that β-barrel membrane proteins come from one ancestor even having different number of sheets which could be added or doubled during evolution. Some studies show a huge sequence conservation among different organisms and also conserved amino acids which hold the structure and help with folding. Note: n and S are, respectively, the number of beta-strands and the "shear number" of

588-549: Is thought to occur through unfolded protein domains in the substrate protein. In HslU, a bacterial ClpX/ClpY homologue of the HSP100 family of AAA proteins, the N- and C-terminal subdomains move towards each other when nucleotides are bound and hydrolysed. The terminal domains are most distant in the nucleotide-free state and closest in the ADP-bound state. Thereby the opening of the central cavity

630-483: The beta-barrel AAA proteins AAA ( A TPases A ssociated with diverse cellular A ctivities ) proteins (speak: triple-A ATPases) are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases , which exert their activity through

672-518: The detergent . For example, the "unfolded" bacteriorhodopsin in SDS micelles has four transmembrane α-helices folded, while the rest of the protein is situated at the micelle-water interface and can adopt different types of non-native amphiphilic structures. Free energy differences between such detergent-denatured and native states are similar to stabilities of water-soluble proteins (< 10 kcal/mol). Refolding of α-helical transmembrane proteins in vitro

714-477: The dif region. Movement toward the dif region is facilitated by the polarity of the KOPS motif. There are three proposed mechanisms of DNA translocation : the rotary inchworm, the staircase, and the revolution mechanism. The rotary inchworm mechanism involves two points of contact between DNA and the subunits of the FtsK C hexamer. These points of contact correspond to an α and a β domain. A conformational change in

756-468: The molten globule states, formation of non-native disulfide bonds , or unfolding of peripheral regions and nonregular loops that are locally less stable. It is also important to properly define the unfolded state . The unfolded state of membrane proteins in detergent micelles is different from that in the thermal denaturation experiments. This state represents a combination of folded hydrophobic α-helices and partially unfolded segments covered by

798-466: The position of the protein N- and C-termini on the different sides of the lipid bilayer . Types I, II, III and IV are single-pass molecules . Type I transmembrane proteins are anchored to the lipid membrane with a stop-transfer anchor sequence and have their N-terminal domains targeted to the endoplasmic reticulum (ER) lumen during synthesis (and the extracellular space, if mature forms are located on cell membranes ). Type II and III are anchored with

840-607: The regulation of gene expression . The AAA proteins contain two domains, an N-terminal alpha/beta domain that binds and hydrolyzes nucleotides (a Rossmann fold ) and a C-terminal alpha-helical domain. The N-terminal domain is 200-250 amino acids long and contains Walker A and Walker B motifs , and is shared in common with other P-loop NTPases, the superfamily which includes the AAA family. Most AAA proteins have additional domains that are used for oligomerization , substrate binding and/or regulation. These domains can lie N- or C-terminal to

882-648: The AAA module. Some classes of AAA proteins have an N-terminal non-ATPase domain which is followed by either one or two AAA domains (D1 and D2). In some proteins with two AAA domains, both are evolutionarily well conserved (like in Cdc48/p97 ). In others, either the D2 domain (like in Pex1p and Pex6p) or the D1 domain (in Sec18p/NSF) is better conserved in evolution. While the classical AAA family

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924-470: The FtsK c hexamer reaches the dif site. FtsK is a part of the divisome of bacteria and coordinates cell division with the resolution of chromosome dimers. FtsK N stabilizes the septum and aids in the recruitment of other proteins to the site of cell division. The N-terminal 220 residues of FtsK are sufficient to promote cell division in Escherichia coli . However, additional evidence suggests that

966-454: The N terminus is not the only part of FtsK that is involved in cell division. In an experiment done by Dubarry, a suppressor mutation allowed the cells to survive without FtsK N . When segments of the FtsK cytoplasmic linker domain were fused to other divisome proteins that can attach to the membrane, such as FtsW, only those fusions that contained the FtsK linker region were able to restore normal cell growth, providing convincing evidence that

1008-454: The Xer recombination. FtsK turns on the activity of XerCD upon expenditure of ATP. The recombination apparatus is made up of four monomers, two being Xer D and two being Xer C, that belong to a family of tyrosine recombinases. The interaction of Xer D and the γ subunit of FtsK C results in the activation of the recombinase. Contact between Xer D and the γ subunit is facilitated by the translocation of DNA. Specifically, translocation stops when

1050-435: The cytoplasmic end of the linker domain, the FtsK C segment of the protein is responsible for enabling the activity of the Xer recombination system upon the formation of a chromosome dimer. Additionally, the FtsK C domain is composed of three subdomains: α, β, and γ. The α and β subunits aggregate to form a hexamer that possesses the ability to translocate DNA through ATP hydrolysis . The ATP hydrolysis sites are found on

1092-643: The energy-dependent remodeling or translocation of macromolecules. AAA proteins couple chemical energy provided by ATP hydrolysis to conformational changes which are transduced into mechanical force exerted on a macromolecular substrate. AAA proteins are functionally and organizationally diverse, and vary in activity, stability, and mechanism. Members of the AAA family are found in all organisms and they are essential for many cellular functions. They are involved in processes such as DNA replication , protein degradation , membrane fusion , microtubule severing , peroxisome biogenesis , signal transduction and

1134-532: The exertion of mechanical force, amplified by other ATPase domains within the same oligomeric structure. The additional domains in the protein allow for regulation or direction of the force towards different goals. AAA proteins are not restricted to eukaryotes . Prokaryotes have AAA which combine chaperone with proteolytic activity, for example in ClpAPS complex, which mediates protein degradation and recognition in E. coli . The basic recognition of proteins by AAAs

1176-483: The linker region of FtsK plays an important role in cell division. Other studies have shown that part of the FtsK N domain (which is in the periplasm) is involved in the construction of the cell wall. FtsK is a member of the AAA motor ATPases. The phylogenetic tree of FtsK originates at the divergence between ssDNA and dsDNA translocases where TraB, FtsK, T4CPs and VirB4s arose. Each of these show structural similarities and

1218-859: The membrane, but do not pass through it. There are two basic types of transmembrane proteins: alpha-helical and beta barrels . Alpha-helical proteins are present in the inner membranes of bacterial cells or the plasma membrane of eukaryotic cells, and sometimes in the bacterial outer membrane . This is the major category of transmembrane proteins. In humans, 27% of all proteins have been estimated to be alpha-helical membrane proteins. Beta-barrel proteins are so far found only in outer membranes of gram-negative bacteria , cell walls of gram-positive bacteria , outer membranes of mitochondria and chloroplasts , or can be secreted as pore-forming toxins . All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism. In addition to

1260-399: The membrane, or the transmembrane segment , is largely hydrophobic and can be visualized using the hydropathy plot . Depending on the number of transmembrane segments, transmembrane proteins can be classified as single-pass membrane proteins , or as multipass membrane proteins. Some other integral membrane proteins are called monotopic , meaning that they are also permanently attached to

1302-446: The membrane. On the cytosolic side, the substrate is ubiquitinated by ER-based E2 and E3 enzymes before degradation by the 26S proteasome. Multivesicular bodies are endosomal compartments that sort ubiquitinated membrane proteins by incorporating them into vesicles. This process involves the sequential action of three multiprotein complexes, ESCRT I to III ( ESCRT standing for 'endosomal sorting complexes required for transport'). Vps4p

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1344-402: The parent branch of FtsK arose along with other branches of TraB, TcpA, and FtsK. Although FtsK has its own phylogeny and branches within, TraB is similar to a sister protein branch that can be traced back to the timeline of FtsK. A common protein that derives from one of the phylogenetic branches of FtsK is SpoIIIE, which is essential for chromosome segregation in some Gram positive bacteria. FtsK

1386-462: The positive inside rule and other methods have been developed. Transmembrane alpha-helical (α-helical) proteins are unusually stable judging from thermal denaturation studies, because they do not unfold completely within the membranes (the complete unfolding would require breaking down too many α-helical H-bonds in the nonpolar media). On the other hand, these proteins easily misfold , due to non-native aggregation in membranes, transition to

1428-463: The protein domains, there are unusual transmembrane elements formed by peptides. A typical example is gramicidin A , a peptide that forms a dimeric transmembrane β-helix. This peptide is secreted by gram-positive bacteria as an antibiotic . A transmembrane polyproline-II helix has not been reported in natural proteins. Nonetheless, this structure was experimentally observed in specifically designed artificial peptides. This classification refers to

1470-690: The protein has to be passed through the ER membrane in a direction dependent on the type. Membrane protein structures can be determined by X-ray crystallography , electron microscopy or NMR spectroscopy . The most common tertiary structures of these proteins are transmembrane helix bundle and beta barrel . The portion of the membrane proteins that are attached to the lipid bilayer (see annular lipid shell ) consist mostly of hydrophobic amino acids. Membrane proteins which have hydrophobic surfaces, are relatively flexible and are expressed at relatively low levels. This creates difficulties in obtaining enough protein and then growing crystals. Hence, despite

1512-432: The significant functional importance of membrane proteins, determining atomic resolution structures for these proteins is more difficult than globular proteins. As of January 2013 less than 0.1% of protein structures determined were membrane proteins despite being 20–30% of the total proteome. Due to this difficulty and the importance of this class of proteins methods of protein structure prediction based on hydropathy plots,

1554-459: The spatial position of the DNA strand. Additionally, the revolution mechanism entails the passing of DNA through a channel formed by the hexameric FtsK C domain. In general, the chromosome dimer is translocated so that the site of resolution is near the divisome and so one copy of the genetic material ends up in each daughter cell. FtsK is the fastest DNA translocation pump, with rates of up to 7 kb s it

1596-443: The translocon (although it would be at the membrane surface or unfolded in vitro ), because its polar residues can face the central water-filled channel of the translocon. Such mechanism is necessary for incorporation of polar α-helices into structures of transmembrane proteins. The amphiphilic helices remain attached to the translocon until the protein is completely synthesized and folded. If the protein remains unfolded and attached to

1638-461: The translocon for too long, it is degraded by specific "quality control" cellular systems. Stability of beta barrel (β-barrel) transmembrane proteins is similar to stability of water-soluble proteins, based on chemical denaturation studies. Some of them are very stable even in chaotropic agents and high temperature. Their folding in vivo is facilitated by water-soluble chaperones , such as protein Skp. It

1680-432: The α subunit can cause the DNA to shift. This shift is followed by a conformational change in the β subunit (which also causes the DNA to move). The repeated conformational changes lead to the translocation of DNA. Conversely, the staircase mechanism sees the α and β subunits of the hexamer interacting with the double-stranded DNA in a sequential and overlapping manner. Conformational changes in each subunit cause movement in

1722-401: The β subunits of the hexamer. The γ domain is responsible for the control of the hexamer. It mediates the attachment of the hexamer to double-stranded DNA, controls the directionality of the translocase , and initiates chromosome dimer segregation. The dif site is found at the intersection between the monomers of the chromosome dimer. It corresponds to where chromosomal replication ceased and

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1764-426: Was based on motifs, the family has been expanded using structural information and is now termed the AAA family. AAA proteins are divided into seven basic clades , based on secondary structure elements included within or near the core AAA fold: clamp loader, initiator, classic, superfamily III helicase, HCLR, H2-insert, and PS-II insert. AAA ATPases assemble into oligomeric assemblies (often homo-hexamers) that form

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