dataesr/scientific-paragraphs-categorization huggingface dataset:
592 he permease unit of the transporter is formed by the heterodimer of LolC and LolE, both of which have MacB/ FtsX-like structure, and in E. coli the LolC-LolE heterodimer cooperates with the NBDs of the ATPase LolD, which provides energy for the lipoprotein extraction. A very similar system is present in A. baumannii, where a homodimeric LolF binds to a dimer of LolD. 593 The structures of the PCD of LolC have been revealed, both in isolation (PDB ID 5NAA  431  and 6F49  432  ) and bound to the periplasmic chaperone LolA (PDB ID 6F3Z)  432  which reveals how a solvent-exposed βhairpin loop (termed the "Hook") and trio of surface residues (the "Pad") of LolC are essential for recruiting LolA from the periplasm and priming it to receive lipoproteins (PDB ID 6F49). 432 he PCD of LolC presents a departure from the prototypical MacB PCD fold, and its SABRE domain has a distinctive β-hairpin structure formed by residues P167-P179 (full-length LolC numbering), which has been named the "hook", which is not observed in the MacB, and which, along with a trio of charged residues from the external side of the SABRE β-barrel, named the "Pad", participates in the LolA recruitment  432  (see Figure  21 above ).
A very similar arrangement is seen in the structure of the related A. baumannii LolF (PDB ID 5UDF) generated from a structural genomics effort Bacillus subtilis and B. amyloliquefaciens produce sporulationdelaying protein (SDP), which is a peptide toxin capable of killing cells within a biofilm to support continued growth, thereby delaying the onset of biofilm sporulation. SDP producing cells protect themselves against the endogenous SDP via the action of the four-component transporter YknWXYZ which acts as a major SDP efflux pump. 568 Within this assembly, the YknYZ forms a noncanonical ABC transporter, where YknZ is the permease, while YknY is the NDB. Heterodimeric assembly of YknY 2 Z 2 forms a transporter remarkably similar to MacB,  579  while the PAP YknX assembles into a hexameric pattern very similar to MacA.
594 Despite the sequence identity of around 20%, the extracellular domain (ED) of the BaYknZ reveals a structure which is virtually identical to that of the PCD of the AaMacB with DaliLite server bringing a Z-score of 20. 1 and structural superposition returning an RMSD of just 1. 6 Å over the C-α backbone of the corresponding domain. 594 imilarly, the structure of the related Gram-positive pump Spr0694-0695, where Spr0695 is the permease and Spr0694 provides the ATPase function, is surprisingly similar to the Gram-negative equivalent (PDB ID 5XU1)  571  and presents PCDs which are virtually identical to those of MacB, suggesting communality of operation, despite the lack of OMF engagement in the respective complex. One small exception is the presence of a well-defined helical loop inserted in the SABRE domain (residues 202-216), which seems to form specific contacts with the TM helices of the transporter and could provide additional conformational coupling or, as suggested by the authors, plays the role of a gating loop.
Numbering these for an isolated PD domain from the N-to the C-terminus, by the respective secondary structure elements, provides a β 1 -α 1 -β 2 -β 3 -α 1 -β 4 configuration, which we refer to as the "standard PD" domain, which is observed in the AcrB PC1 domain  279  (Figure  22 ). The standard PD domain of RND transporters is a version of the ferredoxin-like fold,  595  which is composed of 2 α-helices and 4 β-strands, in an α-β sandwich configuration, with the αhelices being spliced between the β1/β2 and β3/β4, respectively, and the 4 β-strands forming an antiparallel βsheet. The fold has been initially described from the activation domains of pro-carboxypeptidases (e. g. , PDB ID 1NSA  596  and 1AYE  597  ) and a number of RNA-binding proteins, including small nuclear ribonuclear proteins, e.
g. U1A small spliceosomal protein (PDB ID 1URN)  598  and ribosomal protein S6 (PBD ID 1RIS),  599, 600  with the latter showing a β-roll transition of the central sheet. The pore domains of prototypical HAE-1 type transporter such as AcrB,  279  as well as the HME group transporters, such as CusA,  354  contain four variants of the PD fold, namely the PN1, PN2 and PC1, PC2 domains (Figure  5  and Figure  6 ), with PN1 and PC1 being continuous folds, while PN2 and PC2 harbor insertions between their respective β2 and β3 strands, comprising the funnel (FN) domains. 279 These are linked to the substrate engagement by the P1-head domain of the transporter, and similar transitions may occur within other PD-containing transporters, e. g. , the PD-domains of the MacB/ FtsX family. Our analysis of the fold of the globular subdomains that form the funnel or docking domain of the RND transporters reveals that they could be derived from the "standard" PD domain topology by an additional β-hairpin insertion following α2-helix and a flip of the β-hairpin formed by the β2 and β3 strands of the central β-sheet, leading to its disruption.
The central β-sheet is then supplemented during oligomerization, by the equivalent β2-β3 hairpin from the neighboring protomer, providing interconnectivity between the subunits of the functional trimer. As a result of this "hairpin swap", the central continuous β-sheet of the "standard PD domain" is replaced, e. g. , in the DN1 domain of AcrB, by a pseudocontinuous β-sheet, where, due to the outward flip of the β2-β3 hairpin, the antiparallel interface between the cognate β1and β3-strands is substituted by a parallel β1and β3′-strand arrangement (Figure  22 ). A number of RND and related transporters present variations on such an architecture including the HAE-2 family, with representatives such as MmpL3 (PDB ID 6AJF);  277  HAE-3 HpnN (PDB ID 5KHN);  278  and the more distantly related SecDF translocases (e.
g. , PDB ID 3AQP  364  and PBD ID 5YHF  366  ), as well as representatives from eukaryotic groups, such as the human cholesterol transport associated Niemann-Pick disease type C protein 1 (NPC1) (PBD ID: 5JNX  601  and 6W5R  587  ), mouse cholesterol translocator Patched (PBD ID 6MG8),  602  and the human Patched 1 (PDB ID 6OEU  589  and 6DMB 603 ) (Figure  23 ). 5. 7. 6. 1. MmpLs. In Mycobacterium tuberculosis the 14 members of the MmpL (mycobacterial membrane protein large) transporter family form a group of proton-driven carriers, that translocate complex (glyco)lipids and siderophores across the cell envelope. 604, 605 Unlike the RND transporters of the HAE-1 and HME families, these transporters operate as dimers, although some earlier data on the orthologous Corynebacterial CmpLs,  606  namely CmpL1, has suggested a possibility of a trimeric assembly.
Consistent with the prediction, the structure of the isolated D2 domain from the MmpL11 (PDB ID 4Y0L)  609  showed high homology to the PD domains of classical RND transporters. Cross-linking experiments suggest that the orientation of the PD domains in MmpL 11  609  is similar to the PC1/PN2 domain orientation on the AcrB, e. g. (PDB ID 2GIF)  318  or CusA (PDB ID: 4DNT). 610 However, later structures of the MmpL3 from M. smegmatis (PDB IDs 6AJF-6AJJ, 277 6OR2 611 ) display a distinct domelike arrangement. In addition, the PD2 domain of MmpL3 (PDB ID 6OR2) does appear to have a small insert, after β2 (see Figure  25B ). At present there are no experimental structures of PD domains belonging to cluster I MmpLs, although our bioinformatic analysis suggests their insertions are not related to the ones observed in the funnel domains of RND transporters and may be closer related to the α-helical domains observed in the HAE-3.
5. 7. 6. 2. Hopanoid Transporters. The hopanoid transporters, which are representatives of the HAE-3 group and are responsible for the transport of the eponymous pentacyclic triterpenoids with a sterol-like function in the bacterial membrane,  278  also exhibit high similarity to the RND transporters, consistent with that present for PD-like domains. The crystal structure of the HpnN (PDB ID 5KHN)  278  (see Figure  23 ) revealed a dimeric assembly of the transporter, which presented four PD domains, with PD1 and PD2 being equivalent to the classic PD domains observed in HAE-1 and HME RND transporters, but in addition, they present helical inserts forming additional PD3/PD4 domains, with no relation to any hitherto known domains. The splicing of the PD3/PD4 into the PD1 and PD2, respectively, produces the same topology (β 1 -α 1 -β 2 -X-β 3 -α 1 -β 4 ) as discussed above for MmpL and the MacB/FtsX proteins suggesting a general pattern for expanding the architecture (see Figure  25 , panel B).
β 3 ( β 1 -α 1 -β 2 - X-β 3 -α 1 -β 4 ), 5. 7. 6. 3. SecDF. Working in conjunction with the major secretory complex SecYEG/SecA 612 that is driven by SecA ATP-hydrolysis, the proton motive force powered SecDF complex facilitates the threading of the unfolded protein cargoes and plays a chaperone-like function. 365, 613, 614 In Thermus thermophilus SecDF, the SecD and SecF are fused into a single polypeptide chain, and its structure (PDB ID 3AQP)  364  revealed that similar to the group I MmpLs discussed above, SecDF presents a pseudosymmetrical, 12helix transmembrane domain belonging to the RND superfamily and two homologous major periplasmic domains, P1 and P4 (Figure  24  and Figure  25 ). While the P4 domain shows a classic β 1 -α 1 -β 2 -β 3 -α 1 -β 4 organization, similar to the PDdomains in HAE-1 PD and MmpL3, the P1 domain presents a β 1 -α 1 -β 2 -X-β 3 -α 1 -β 4 organization , where "X" is a large insert forming the so-called "head" subdomain, while the core PD β-strands form the cores of both the P1 and P4 form a pseudosymmetrical 8-stranded antiparallel β-sheet that covers the TM region of SecDF and is planar in the most structures, including P1-membrane facing "F" forms and P1-outward facing "I"-forms; 364,615 however, unexpectedly, the PDdomains of the transporter were also revealed in a β-barrel form (known as Super F-form) (PDB ID 5YHF).
366 The βbarrelled super F-form is speculated to engage with the emergent preprotein coming out of the SecYEG on the periplasmic side of the membrane, which is bound to the P1head. The conformational transition from super F-to-F and planification of the β-sheet is speculated to be associated with substrate dragging, and consistent with such interpretation, fixing the β-sheet by cross-linking between the interface of the P1-base and P4 abolished the translocation activity of SecDF, suggesting that β-sheet rearrangement occurs during protein translocation. 615 Further transition of the F to I-form is associated with the formation of a proton-accessible tunnel in the TM-part of the protein (as seen in PDB ID 5XAN) and subsequent release of the cargo, leaving the P1-head outward facing in the cargo-disengaged "I without tunnel form" 366 (Figure  24 ).
617 Patched (PTCH1) and Dispatched (DISP) belong to the eukaryotic dispatched RND transporter family. Both are involved in the hedgehog signaling pathway, during embryogenesis and tissue homeostasis, where Dispatched exports the N-terminal portion of sonic hedgehog, with C-terminally linked cholesterol,  274, 618, 619  and PTCH1 acts as a receptor of the lipidated sonic hedgehog protein, binding of which releases the downstream suppression of Smoothened (SMO). Cryo-EM structures of monomeric human PTCH1 resemble the architecture of NPC1 (PDB ID 6OEU, 6OEV; 589 6DMB  603  ), presenting an RMSD of ∼2. 5 Å, and recently the structure of the human Dispatched-1 (DISP1) homologue has been obtained (PDB ID 6XE6. 590 These eukaryotic homologues possess two separate PD domains, which are decorated in a similar fashion to the ones discussed above for the Cluster I MmpLs and Hopanoid transporters.
Notably, the two PD-like domains of NPC1, named the middle luminal domain (MLD) and C-terminal luminal domain or Cys-rich domain (CTD), present large insertions between the β 2 -β 3 (PDB ID 5U74),  586  an organization which is also shared by the Patched structure. 589, 603 In addition, the NPC1 MLD-domain (PD1) contains a β-hairpin insertion between β1 and α1, which mimics the ones observed in the FtsX members such as discussed previously (Figure  25  and Figure  21 ). A very similar insertion is seen in the extracellular domain 2 (ECD2/PD2) of the DISP1 (PDB ID 6XE6)  590  but not in the PTCH1. Taken together, the analysis of the PD domains of the RNDlike transporters presented, as well as the FtsX/MacB family, displays a clear pattern of usage and modification of the PD modules, with two "hotspots" of insertion being utilizedthe first one is located at the tip of the β 2 -β 3 hairpin of the central PD-β sheet and allows for splicing of large subdomains, e.
g. , the SABRE domain in the case of the FtsX/MacB family, or the large helical subdomain inserts in the case of PD3/PD4 domains of the hopanoid transporters and the eukaryotic RND-like transporters (NPC1/DISP1/PTCH1). The second insertion point accommodates smaller splice-ins in the form of an additional β-hairpin insertion, as seen in the S. pneumoniae FtsX (PDB ID 6HE6); the ECD2 of DISP (PDB ID 6XE6),   24  MlaE (PDB ID 6XBD),  439  LptB2FGC complex (PDB ID 6S8N),  635  Wzm-WznT (PDB ID 6M96),  429  and ABCG2 (PDB ID 5NJG). 632 Top-down view from the periplasm. Note: due to the intertwisting of the helices in the type IV transporters, the diagram depends on the level at which the slice is cut through the TM; the provided view is representative to the middle of TM segment, based on the ABCB1 structure (PDB ID 6QEX).
Finally, the SecDF presents a unique insertion in its first PD-domain, with the P1-head domain being spliced after α2 (see Figure  25 ). Notably the architecture seen in the PD domains is also present in a number of additional periplasmic proteins which lack transporter function, e. g. , the two-component signaling modulator family of MzrA proteins (PDB ID 4PWU),  620  as well as more distantly related proteins including the archaeal Tk-subtilisin chaperone pro-peptides (PDB ID 3A3O) and,  621  similarly, chaperoning activation domains of carboxypeptidases (PDB ID 1PBA),  622  as well as acylphosphatases (e. g. , mtAcP PDB ID 1APS)  623  and the aforementioned small nuclear ribonuclear proteins such as U1-SNRP A (PBD ID 3G8T, 624 3UCU 625 ) (see Figure  21B ). 5. 7. 7. Relations of the Membrane Porter Domains of MacB/FtsX to Other ABC Transporter Families.
At first sight, there appears to be limited similarity between the porter domains of MacB/FtsX containing 4-TMs and the more typical ABC transporters, which contain 6-TMs as standard. However, closer inspection of the MacB-TM regions utilizing DALI pairwise fold-comparison software  24  and comparison against different members of the type IV family, such as ABCB1 (PDB ID 4M1M, 626 3G60 627 ), heterodimeric TmrAB (PDB ID 5MKK), and the ADP-bound form of the lipid-linked oligosaccharide flippase PglK (PDB ID: 5NBD),  628  reveal unexpectedly high similarity of the MacB/FtsX family to this family, with the ABCB1 returning a Z-score of 8. 7 (PDB ID 3G60), based on the superposition of the first three N-terminal helices (TM 1-3) of the type IV transporters showing high structural similarity to the MacB TM helices 1-3.
Despite this similarity, it has to be noted that the dimer interface of MacB is not matched with the dimer interface presented by the structures of type IV ABC transporters, e. g. in the MacB/FtsX TM helices 1-3 do not form part of the substrate binding cavity and are hence more likely to play a role in energy transduction, rather than substrate interactions, while in type IV helices 1-3 face away from the central cavity toward the lipid bilayer  24  (Figure  26 , panel A, showing the packing in ABCB1 6QEX  521  ). An expanded topological analysis of the type VII ABC-family topological relationships, which in addition to the type IV transporters discussed above also included type I importers (e. g. , MetNI(Q) (PDB ID 3DHW),  629  YjgP/YjgQ (LptBFG; type VI family)),  630, 631  as well as the members of type V exporters, such as the ABCG  582, 632  and ABCA  633  involved in eukaryotic lipid export, revealed unexpected similarities, suggesting that they might be evolutionarily related.
634 Based on these similarities, an alternative classification of ABC transporter topologies has been proposed, with the core of these transporters' structures consisting of the four-TM core segments (1-4), as observed in the MacB/FtsX family (e. g. , PDB ID 5WS4), and it has been proposed that MacB/FtsX (Group VII) may be a basal group of transporters from which the other topologies covering groups V, VI, and even IV are derived. Uniquely, the MacB/FtsX family additionally possesses a second coupling helix (CH2) at the C-terminal end of the fourth core TM segment (Figure  26 , panel B; TMsegment is colored red), which is not present in the TMDs of LptBFG (YjgP/YjgQ; type VI) or in group V (ABCG and ABCA) transporters. 634 ntriguingly, the complete topology of type IV floppase/ exporters (formerly type I exporters) could also be derived when using MacB/FtsX as a basis, as TM segments 1, 2, 3, and 6 can be structurally aligned to the TMs 1-4 of MacB.
Insertion of TM helices 4-5 carrying a canonical coupling helix between TM3 and 4 of MacB/FtsX produces a topology equivalent to the type IV floppase/exporters. Consistent with this, DALI superposition of MacB (PDB ID 5WS4) with type IV heterodimeric exporter TmrAB (PDB ID 5MKK),  523  which is a homologue of the antigen translocation complex TAP, returned a Z-score of 7. 7. 24 While intriguing and appealing in its simplicity, such systematics do not automatically suggest that the MacB/FtsX family is a basal group, as it could be a product of degenerative evolution. More recently, Murakami et al. 580  also extended their DALI analysis to the type V family members ABCG2 (PDB ID 5NJG)  632  and ABCA1 (PDB ID 5XJY)  633  that returned high Z-score values of 7. 6 and 7. 5, respectively. While the overall score is lower, these transporters allow better superposition, covering all four TMs of MacB, and importantly, they provide a dimer interface matching that of the MacB.
MacB can therefore be considered the "holotype" for the whole of the type VII ABC transporter superfamily  428, 431  and has become the first structurally characterized member of the ABC3 superfamily of the ABC transporters as defined by Wang et al. 427  Its unique architecture suggests a mechanistically distinct functional cycling mechanism. The EcMacB has been revealed in a nucleotide free form (PDB ID 5NIK), with the NBDs apart and unable to bind ATP. 272 However, an ATP-bound (PDB ID 5LJ7) and nonhydrolyzable ATP-analogue bound form (PDB ID 5LJ6, 5LOL)  431  have also been reported. For AaMacB and AbMacB, an ADP-analogue bound form (e. g. , adenosine-5′-(β-thio)diphosphate (PDB ID 5WS4)) and a nucleotide-free form (PDB ID 5GKO) have been obtained, respectively. 24 In addition, the structure of the Streptococcal MacB-like transporter Spr0694-0695 (PDB ID 5XU1)  571  was revealed in a nucleotide-free state and the comparative analysis of these structures has allowed us to reconstruct a plausible energycoupling cycle of the MacB/FtsX-like transporters.
5. 7. 9. Substrate Binding Site. In the MacB/FtsX family, the extra-membrane extensions of TM1 and TM2 protrude out of the membrane forming a kinked, "Y-shaped" conformation with a small semioccluded cavity, that is accessible from the periplasm. In the cryo-EM structure of MacB (PDB ID 5NIL), an unidentified electron density, occluding this region between the periplasmic extensions of TM1 and TM2, has been reported. 272 Although, the low resolution of the associated cryo-EM map (at 5. 3 Å) did not permit a clear interpretation, it has been speculated that it might represent a putative substrate binding site. 272 While there is no direct structural data on substrate binding, structure-guided mutagenesis was used to narrow down the potential substrate binding residues,  431  showing a plausible erythromycin binding site, covering predominantly bulky hydrophobic residues (including Y315, F320, F320, F503, and M507), mapping mostly to the PD-subdomain facing the interdomain interface.
Unlike the αand βdomains, the equatorial domain does not appear to be a duplication of the same structural pattern. Despite the strong structural analogy of OprM (PDB code: 3D5K) with its counterparts (TolC, PDB code: 1EK9; VceC, PDB code: 1YC9; CmeC, PDB code: 4MT4; CusC, PDB code: 3PIK), the identity of their primary sequence is rather low (19% for TolC and 23% for VceC). A multiple alignment of OprM and OMPs from different species highlights the residues conserved during evolution (Figure  29A ). These residues, which probably play a key role in the structure or function of OMPs of the TolC family, have a preferential distribution at the ends of the α-helices and at the level of the connections between the α-domain and the β-domain. Furthermore, the majority of the conserved residues are located on the C-terminal motif which could be an evolutionarily ancestral sequence.
Rapid advances in the structural characterization of the PAP proteins over the past decade have shed light on all of the main group members, although the RND-associated proteins were the first to be solved; for exampel, MexA (PDB ID 1T5E;  733, 734  PBD ID 2V4D  716  ) and AcrA (PDB ID 2F1M  735  ) remain the best-studied examples due to the plethora of structures of assembled tripartite complexes with their participation. 270, 287, 305, 306.
BD been resolved both in isolation, e. g. , the copper-efflux associated CusB (PDB ID 3H94 3OOC, 3OPO, 3OW7)  702  and ZneB from Cupriavidus metallidurans (PDB ID 3LLN),  63  and in complex with cognate transporters, e. g. CusBA (PDB ID 4DNR, 3T51, 3T53, 3T56, 3NE5, 4DNT, 4DOP). 359, 610 he structures of MacB-associated PAPs from E. coli EcMacA (PDB ID 3FPP)  736  and Aggregatibacter (Actinobacillus) actinomycetemcomitans AaMacA (PDB ID 4DK0)  737  and the structure of the full MacAB-TolC pump have been reconstructed from cryo-EM data (PDB ID 5NIL-5NIK). 272 he structures of the PAPs associated with the MacB-type Gram-positive efflux systems have also been resolved, including the Bacillus YknX  594  and the Spr0693 from Streptococcus pneumoniae R6 (PDB ID 5XU0),  571  both of which assemble into a hexameric pattern very similar to MacA.
The first MFS transporter-associated PAP was EmrA from Aquifex aeolicus (PDB ID 4TKO). 738 The last group of PAPs to reveal their structure was the PAPs associated with T1SS. The structure of E. coli HlyD (PDB ID 5C21, 5C22)  739  was followed by the Serratia marcescens LipC PAP (PDB ID 5NEN). 514 n addition, the structures of some aberrant PAPs have become available, such as the PAP BesA from the Lyme disease associated spirochete Borrelia burgdorferi (PDB ID 4KKS-4KKU),  703  which lacks the helical hairpin domain altogether. In addition, some orphan PAP structures could also be found in the database, as a result of structural genomics efforts, e. g. , BACEGG_01895) from a putative efflux pump from Bacteroides eggerthii DSM 20697 (PDB ID 4L8J); however, its association with HAE-1 or HME pumps remains to be established.
T1SS Associated PAPs Similar to the PAPs associated with the MFS assemblies, the structure of the representative T1SS-associated PAP, namely E. coli HlyD (referred to as EcHlyD henceforth) from the αhemolysin secretion system, presents an architecture lacking an MPD and is characterized by an oversized α-helical hairpin domain measuring ∼115 Å in length, thus being second only to the MFS-associated EmrA, which is almost 130 Å long (PDB ID 5C21-5C2). 739 imilar to AaEmrA discussed above, the α-helical hairpin domain of EcHlyD is divided roughly in the middle, into an Nterminal and C-terminal part, by a loop at its distal tip (L2), which is supposed to contact the OMF. Unlike the MFSassociated PAPs, however, which have two continuous αhelices forming each half of the α-hairpin domain, the HlyD hairpin presents a complex, discontinuous architecture, which deviates from the standard coiled-coils observed in the classical RND-associated transporters and is composed of three helical fragments (α1 to α3), linked by two connecting loops L1 and L2.