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1.  Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex 
eLife  null;3:e05115.
The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) that functions in early autophagy consists of the lipid kinase VPS34, the scaffolding protein VPS15, the tumor suppressor BECN1, and the autophagy-specific subunit ATG14. The structure of the ATG14-containing PI3KC3-C1 was determined by single-particle EM, revealing a V-shaped architecture. All of the ordered domains of VPS34, VPS15, and BECN1 were mapped by MBP tagging. The dynamics of the complex were defined using hydrogen–deuterium exchange, revealing a novel 20-residue ordered region C-terminal to the VPS34 C2 domain. VPS15 organizes the complex and serves as a bridge between VPS34 and the ATG14:BECN1 subcomplex. Dynamic transitions occur in which the lipid kinase domain is ejected from the complex and VPS15 pivots at the base of the V. The N-terminus of BECN1, the target for signaling inputs, resides near the pivot point. These observations provide a framework for understanding the allosteric regulation of lipid kinase activity.
DOI: http://dx.doi.org/10.7554/eLife.05115.001
eLife digest
To survive starvation and other hard times, cells have developed a unique recycling strategy: they can scavenge the resources they need from within the cell itself. To do this, the cell forms a double-layered envelope around particular sections of the cell to seal them off from the rest. Then, the contents of the envelope are taken apart and the resulting raw materials are sent elsewhere in the cell where they can be used as required. This process is called autophagy.
In more complex organisms like humans, autophagy can have additional roles. One of the key proteins involved in autophagy—called BECN1—suppresses the growth of tumors, and the gene that makes BECN1 is missing in 40–70% of human breast, ovarian, and prostate cancers. Autophagy may also help to prevent Huntington's disease and other similar conditions by stopping disease-causing proteins or broken cell parts from building up inside brain cells.
The BECN1 protein does not work alone. Instead, it becomes part of a group, or ‘complex’, of several proteins that are required to form the envelope made during autophagy. However, the three-dimensional structure of the protein complex is unclear.
Baskaran et al. used electron microscopy and other techniques to investigate this structure and found that the complex forms a V shape with two arms, which is held together by its largest protein, VPS15. This protein also acts as a bridge between BECN1 and another protein that is a target for new cancer drugs, called VPS34.
Next, Baskaran et al. used a different set of techniques to determine how the complex moves. This revealed that many of the connections between proteins in the complex are flexible. However, one of the arms is inflexible and this limits the ability of the VPS34 protein to move. Understanding this structural constraint may help us to design drugs that are able to target the protein complex more efficiently.
DOI: http://dx.doi.org/10.7554/eLife.05115.002
doi:10.7554/eLife.05115
PMCID: PMC4281882  PMID: 25490155
autophagy; three dimensional electron microscopy; hydrogen–deuterium exchange; protein kinase; lipid kinase; Human
2.  The beginning of the end: How scaffolds nucleate autophagosome biogenesis 
Trends in cell biology  2013;24(1):10.1016/j.tcb.2013.07.008.
Autophagy is a conserved mechanism that is essential for cell survival in starvation. Moreover, autophagy maintains cellular health by clearing unneeded or harmful materials from cells. Autophagy proceeds by the engulfment of bulk cytosol and organelles by a cup-shaped double membrane sheet known as the phagophore. The phagophore closes upon itself to form the autophagosome, which delivers its contents to the vacuole or lysosome for degradation. A multiprotein complex consisting of the protein kinase Atg1 together with Atg13, Atg17, Atg29, and Atg31 (ULK1, ATG13, FIP200, and ATG101 in humans) has a pivotal role in the earliest steps of this process. This review summarizes recent structural and ultrastructural analysis of the earliest step in autophagosome biogenesis and discusses a model in which the Atg1 complex clusters high curvature vesicles containing the integral membrane protein Atg9, thereby initiating the phagophore.
doi:10.1016/j.tcb.2013.07.008
PMCID: PMC3877172  PMID: 23999079
SNAREs; Atg1; Atg9; Atg13; autophagy; ULK1; membrane bending; vesicle tethering
3.  What the N-terminal domain of Atg13 looks like and what it does 
Autophagy  2013;9(7):1112-1114.
Atg13 is a subunit of the Atg1 complex that is involved in autophagy. The middle and C-terminal regions of Atg13 are intrinsically disordered and rich in regulatory phosphorylation sites. Thus far, there have been no structural data for any part of Atg13, and no function assigned to its N-terminal domain. We crystallized this domain, and found that it has a HORMA (Hop1, Rev7, Mad2) fold. We showed that the Atg13 HORMA domain is required for autophagy and for recruitment of the phosphatidylinositol (PtdIns) 3-kinase subunit Atg14, but is not required for Atg1 interaction or Atg13 recruitment to the PAS. The HORMA domain of Atg13 is similar to the closed conformation of the spindle checkpoint protein Mad2. A pair of conserved arginines was identified in the structure, and tested functionally in yeast. These residues are important for autophagy, as mutations abrogate autophagy and block Atg14 recruitment. The location of these Arg residues in the structure suggests that the Atg13 HORMA domain could act as a phosphorylation-dependent conformational switch.
doi:10.4161/auto.24896
PMCID: PMC3722324  PMID: 23670046
Atg13; HORMA; Atg14; protein structure; protein crystallography; yeast genetics; protein degradation
4.  How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4 
eLife  2014;3:e01754.
The Nef protein of HIV-1 downregulates the cell surface co-receptor CD4 by hijacking the clathrin adaptor complex AP-2. The structural basis for the hijacking of AP-2 by Nef is revealed by a 2.9 Å crystal structure of Nef bound to the α and σ2 subunits of AP-2. Nef binds to AP-2 via its central loop (residues 149–179) and its core. The determinants for Nef binding include residues that directly contact AP-2 and others that stabilize the binding-competent conformation of the central loop. Residues involved in both direct and indirect interactions are required for the binding of Nef to AP-2 and for downregulation of CD4. These results lead to a model for the docking of the full AP-2 tetramer to membranes as bound to Nef, such that the cytosolic tail of CD4 is situated to interact with its binding site on Nef.
DOI: http://dx.doi.org/10.7554/eLife.01754.001
eLife digest
Infection by a pathogen, such as a bacterium or virus, activates both the innate immune response—which is immediate but not specific to the pathogen—and the adaptive immune response, which is stronger and specific to the pathogen. White blood cells called CD4+ T helper cells play an important role in the early stages of the adaptive immune response by helping to activate and regulate other white blood cells that go on to eradicate the pathogen.
HIV-1 is a retrovirus that infects immune cells that have the CD4 receptor on their surface, including CD4+ T helper cells. As the number of worker CD4+ T helper cells falls, the adaptive immune response gradually weakens, and the HIV-1 infected individual becomes increasingly susceptible to infection and disease. An individual is said to develop AIDS when either their CD4+ T helper cell count falls below 200 cells per microliter or they begin to experience specific diseases associated with the HIV-1 infection.
In an effort to prevent and treat AIDS, researchers have worked to understand the HIV-1 genome and have developed medicines that target the enzymatic activity of viral proteins involved in viral replication. When used in combination, these drugs have helped to reduce transmission of HIV-1, and also to reduce deaths from the disease. However, worries about side effects and drug resistance mean that there is a need to develop new drugs.
The HIV-1 genome codes for a number of accessory proteins, including a protein known as Nef that attacks the CD4+ T helper cells, removing the CD4 protein that gives the cells their name. This reduces the ability of the T cells to activate the immune system and allows the virus to spread. Nef acts by forming a complex with a protein called AP-2 in the T cells, and this complex then interacts with the CD4 proteins, causing them to be internalized and then destroyed inside the cells.
Ren et al. have now worked out the structure of the Nef:AP-2 complex at the molecular level and identified the amino acid residues within the Nef protein that interact with the AP-2 protein. This allowed Ren et al. to propose a detailed model of the interaction between the complex and the CD4 protein, and how this leads to the protein being destroyed. This information could be used to develop drugs that work by blocking the amino residues on AP-2 that bind to Nef. Moreover, since these sites are not susceptible to rapid mutations, such drugs are less likely to encounter the problem of drug resistance.
DOI: http://dx.doi.org/10.7554/eLife.01754.002
doi:10.7554/eLife.01754
PMCID: PMC3901399  PMID: 24473078
HIV-1; protein crystallography; membrane traffic; human
5.  How Atg18 and the WIPIs sense phosphatidylinositol 3-phosphate 
Autophagy  2012;8(12):1851-1852.
The key autophagic lipid sensors are Atg18 in yeast and the WIPI proteins in mammals. Atg18 and the WIPIs belong to the PROPPIN family of proteins. PROPPINs are seven- bladed β-propellers that bind to phosphatidylinositol 3-phosphate (PtdIns3P) and phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2]. In order to understand how PROPPINs bind phosphoinositides, we have determined the crystal structure of a representative, biochemically tractable PROPPIN, Hsv2 of Kluveromyces lactis. The structure revealed that PROPPINs contain two phosphoinositide binding sites which cooperate with a hydrophobic anchoring loop in membrane binding. These three binding elements cooperate in function, as demonstrated by the incremental loss of function in Atg18 mutants impaired in combinations of the two phosphoinositide binding sites and the hydrophobic loop.
doi:10.4161/auto.22077
PMCID: PMC3541302  PMID: 22996041
Atg18; Atg21; WIPI; autophagy; membrane binding
6.  Novel Fold and Maturation Pathway of a dsRNA Virus Capsid 
Structure (London, England : 1993)  2013;21(8):1374-1383.
The cystovirus ϕ6 shares several distinctive features with other double-stranded RNA viruses, including the human pathogen, rotavirus: segmented genomes; non-equivalent packing of 120 subunits in its icosahedral capsid; capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with a novel α-helical fold. We also solved the procapsid by cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation which is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine.
doi:10.1016/j.str.2013.06.007
PMCID: PMC3742642  PMID: 23891288
Bacteriophage ϕ6; Cystoviridae; cryo-electron microscopy; capsid structure; capsid expansion; segmented genome; conformational change; RNA packaging
7.  Structural Basis for Recruitment and Activation of the AP-1 Clathrin Adaptor Complex by Arf1 
Cell  2013;152(4):755-767.
Summary
AP-1 is a clathrin adaptor complex that sorts cargo between the trans-Golgi network and endosomes. AP-1 recruitment to these compartments requires Arf1-GTP. The crystal structure of the tetrameric core of AP-1 in complex with Arf1-GTP, together with biochemical analyses, shows that Arf1 activates cargo binding by unlocking AP-1. Unlocking is driven by two molecules of Arf1 that bridge two copies of AP-1 at two interaction sites. The GTP-dependent switch I and II regions of Arf1 bind to the N-terminus of the β1 subunit of one AP-1 complex, while the back side of Arf1 binds to the central part of the γ subunit trunk of a second AP-1 complex. A third Arf1 interaction site near the N-terminus of the γ subunit is important for recruitment, but not activation. These observations lead to a model for the recruitment and activation of AP-1 by Arf1.
doi:10.1016/j.cell.2012.12.042
PMCID: PMC3913725  PMID: 23415225
8.  Architecture of the Atg17 Complex as a Scaffold for Autophagosome Biogenesis 
Cell  2012;151(7):1501-1512.
SUMMARY
Macroautophagy is a bulk clearance mechanism in which the double-membraned phagophore grows and engulfs cytosolic material. In yeast, the phagophore nucleates from a cluster of 20-30 nm diameter Atg9-containing vesicles located at a multiprotein assembly known as the preautophagosomal structure (PAS). The crystal structure of a 2:2:2 complex of the earliest-acting PAS proteins, Atg17, Atg29, and Atg31, was solved at 3.05 Å resolution. Atg17 is crescent-shaped with a 10 nm radius of curvature. Dimerization of the Atg17-Atg31-Atg29 complex is critical for both PAS formation and autophagy and each dimer contains two separate and complete crescents. Upon induction of autophagy, Atg17-Atg31-Atg29 assembles with Atg1 and Atg13, which in turn initiates the formation of the phagophore. The C-terminal EAT domain of Atg1 was shown to sense membrane curvature, dimerize, and tether lipid vesicles. These data suggest a structural mechanism for the organization of Atg9 vesicles into the early phagophore.
doi:10.1016/j.cell.2012.11.028
PMCID: PMC3806636  PMID: 23219485
9.  Two-Site Recognition of Phosphatidylinositol 3-Phosphate by PROPPINs in Autophagy 
Molecular cell  2012;47(3):339-348.
SUMMARY
Macroautophagy is essential to cell survival during starvation and proceeds by the growth of a double-membraned phagophore, which engulfs cytosol and other substrates. The synthesis and recognition of the lipid phosphatidylinositol 3-phosphate (PI(3)P) is essential for autophagy. The key autophagic PI(3)P sensors, which are conserved from yeast to humans, belong to the PROPPIN family. Here we report the crystal structure of the yeast PROPPIN Hsv2. The structure consists of a seven-bladed β-propeller, and unexpectedly, contains two pseudo-equivalent PI(3)P binding sites on blades 5 and 6. These two sites both contribute to membrane binding in vitro and are collectively required for full autophagic function in yeast. These sites function in concert with membrane binding by a hydrophobic loop in blade 6, explaining the specificity of the PROPPINs for membrane-bound PI(3)P. These observations thus provide a structural and mechanistic framework for one of the conserved central molecular recognition events in autophagy.
doi:10.1016/j.molcel.2012.05.027
PMCID: PMC3595537  PMID: 22704557
10.  COORDINATED ACTIVATION OF THE RAC-GAP β2-CHIMAERIN BY AN ATYPICAL PROLINE-RICH DOMAIN AND DIACYLGLYCEROL 
Nature communications  2013;4:1849.
Chimaerins, a family of GTPase activating proteins (GAPs) for the small G-protein Rac, have been implicated in development, neuritogenesis, and cancer. These Rac-GAPs are regulated by the lipid second messenger diacylglycerol (DAG) generated by tyrosine-kinases such as the epidermal growth factor receptor (EGFR). Here we identify an atypical Pro-rich motif in chimaerins that binds to the adaptor protein Nck1. Unlike most Nck1 partners, chimaerins bind to the third SH3 domain of Nck1. This association is mediated by electrostatic interactions of basic residues within the Pro-rich motif with acidic clusters in the SH3 domain. EGF promotes the binding of β2-chimaerin to Nck1 in the cell periphery in a DAG-dependent manner. Moreover, β2-chimaerin translocation to the plasma membrane and its peripheral association with Rac1 requires Nck1. Our studies underscore a coordinated mechanism for β2-chimaerin activation that involves lipid interactions via the C1 domain and protein-protein interactions via the N-terminal Pro-rich region.
doi:10.1038/ncomms2834
PMCID: PMC3700536  PMID: 23673634
11.  Membrane budding and scission by the ESCRT machinery: it's all in the neck 
The endosomal sorting complexes required for transport (ESCRTs) catalyze one of the most unusual membrane remodelling events in cell biology. ESCRT-I and ESCRT-II direct membrane budding away from the cytosol by stabilizing bud necks without coating the bud and without being consumed in the buds. ESCRT-III cleaves the bud necks from their cytosolic face. ESCRT-III-mediated membrane neck cleavage is crucial for many processes, including the biogenesis of multivesicular bodies, viral budding, cytokinesis, and probably autophagy. Recent studies of ultrastructures induced by ESCRT-III overexpression in cells and the in vitro reconstitution of the budding and scission reactions have led to breakthroughs in understanding these remarkable membrane reactions.
doi:10.1038/nrm2937
PMCID: PMC2922035  PMID: 20588296
12.  Self-eating with your fingers 
Cell Research  2012;22(5):783-785.
doi:10.1038/cr.2012.39
PMCID: PMC3343659  PMID: 22410794
13.  The circuitry of cargo flux in the ESCRT pathway 
The Journal of Cell Biology  2009;185(2):185-187.
The endosomal sorting complex required for transport (ESCRT) complexes sort ubiquitinated membrane proteins into multivesicular bodies, which is a key step in the lysosomal degradation pathway. Shields et al. (Shields, S.B., A.J. Oestreich, S. Winistorfer, D. Nguyen, J.A. Payne, D.J. Katzmann, and R. Piper. 2009. J. Cell Biol. 185:213–224) identify a new ubiquitin-binding site in ESCRT-I and provide evidence that the upstream ESCRT-I and -II complexes sort cargo in parallel rather than in series.
doi:10.1083/jcb.200903013
PMCID: PMC2700367  PMID: 19380875
14.  Regulation of Protein Kinases by Lipids 
Membranes are sites of intense signaling activity within the cell, serving as dynamic scaffolds for the recruitment of signaling molecules and their substrates. The specific and reversible localization of these signaling molecules to membranes is critical for the appropriate activation of downstream signaling pathways. Phospholipid-binding domains, including C1, C2, PH, and PX domains, play critical roles in the membrane targeting of protein kinases. Recent structural studies have identified a new membrane association domain, the Kinase Associated 1 (KA1) domain, which targets a number of yeast and mammalian protein kinases to membranes containing acidic phospholipids. Despite an abundance of localization studies on lipid-binding proteins and structural studies of the isolated lipid-binding domains, the question of how membrane binding is coupled to the activation of the kinase catalytic domain has been virtually untouched. Recently, structural studies on protein kinase C (PKC) have provided some of the first structural insights into the allosteric regulation of protein kinases by lipid second messengers.
doi:10.1016/j.sbi.2011.07.006
PMCID: PMC3232407  PMID: 22142590
15.  Molecular basis for SNX-BAR-mediated assembly of distinct endosomal sorting tubules 
The EMBO Journal  2012;31(23):4466-4480.
A systematic analysis of the dimerization, membrane remodelling and higher order assembly properties of all 12 human SNX-BAR sorting nexins reveals how different SNX-BAR combinations allow the formation of distinct tubular subdomains from the same endosomal vacuole during cargo sorting.
Sorting nexins (SNXs) are regulators of endosomal sorting. For the SNX-BAR subgroup, a Bin/Amphiphysin/Rvs (BAR) domain is vital for formation/stabilization of tubular subdomains that mediate cargo recycling. Here, by analysing the in vitro membrane remodelling properties of all 12 human SNX-BARs, we report that some, but not all, can elicit the formation of tubules with diameters that resemble sorting tubules observed in cells. We reveal that SNX-BARs display a restricted pattern of BAR domain-mediated dimerization, and by resolving a 2.8 Å structure of a SNX1-BAR domain homodimer, establish that dimerization is achieved in part through neutralization of charged residues in the hydrophobic BAR-dimerization interface. Membrane remodelling also requires functional amphipathic helices, predicted to be present in all SNX-BARs, and the formation of high order SNX-BAR oligomers through selective ‘tip–loop' interactions. Overall, the restricted and selective nature of these interactions provide a molecular explanation for how distinct SNX-BAR-decorated tubules are nucleated from the same endosomal vacuole, as observed in living cells. Our data provide insight into the molecular mechanism that generates and organizes the tubular endosomal network.
doi:10.1038/emboj.2012.283
PMCID: PMC3512392  PMID: 23085988
BAR domain; phosphoinositide; retromer; sorting nexin; VPS35
16.  Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes 
PLoS Computational Biology  2012;8(10):e1002736.
The formation of vesicles is essential for many biological processes, in particular for the trafficking of membrane proteins within cells. The Endosomal Sorting Complex Required for Transport (ESCRT) directs membrane budding away from the cytosol. Unlike other vesicle formation pathways, the ESCRT-mediated budding occurs without a protein coat. Here, we propose a minimal model of ESCRT-induced vesicle budding. Our model is based on recent experimental observations from direct fluorescence microscopy imaging that show ESCRT proteins colocalized only in the neck region of membrane buds. The model, cast in the framework of membrane elasticity theory, reproduces the experimentally observed vesicle morphologies with physically meaningful parameters. In this parameter range, the minimum energy configurations of the membrane are coatless buds with ESCRTs localized in the bud neck, consistent with experiment. The minimum energy configurations agree with those seen in the fluorescence images, with respect to both bud shapes and ESCRT protein localization. On the basis of our model, we identify distinct mechanistic pathways for the ESCRT-mediated budding process. The bud size is determined by membrane material parameters, explaining the narrow yet different bud size distributions in vitro and in vivo. Our membrane elasticity model thus sheds light on the energetics and possible mechanisms of ESCRT-induced membrane budding.
Author Summary
Lipid membranes enclose the cytosol of biological cells and compartmentalize their interior. Vesicles are used to transport membrane proteins between cellular compartments. The ESCRT protein machinery induces the creation of such vesicles away from the cytosol. The resulting vesicles are uncoated by protein. Upon vesicle scission and release into the endosome, the ESCRT proteins are recycled into the cytosol. We develop a membrane-elasticity model that captures this budding process. The model reproduces the vesicle morphologies observed in fluorescence microscopy images, and identifies the energetic driving force of vesiculation. We also characterize possible mechanisms of ESCRT-induced membrane budding. The size of the resulting vesicles is determined by membrane material parameters, explaining the narrow yet different bud size distributions in vitro and in vivo. Our membrane elasticity model thus provides insight into the energetics and mechanisms of uncoated vesicle formation.
doi:10.1371/journal.pcbi.1002736
PMCID: PMC3475702  PMID: 23093927
17.  Proline-rich regions and motifs in trafficking: From ESCRT interaction to viral exploitation 
Traffic (Copenhagen, Denmark)  2011;12(10):1282-1290.
Most membrane enveloped viruses bud from infected cells by hijacking the host ESCRT machinery. The ESCRTs are recruited to bud sites by viral proteins that contain short proline-rich motifs (PRMs) known as late domains. The late domains probably evolved by co-opting host PRMs involved in the normal functions of ESCRTs in endosomal sorting and cytokinesis. The solution and crystal structures of PRMs bound to their interaction partners explain the conserved roles of Pro and other residues that predominate in these sequences. PRMs are often grouped together in much larger proline-rich regions (PRRs) of as many as 150 residues. The PRR of the ESCRT-associated protein ALIX autoregulates its conformation and activity. The robustness of different viral budding and host pathways to impairments in proline-based interactions varies considerably. The known biology of proline rich motif recognition in the ESCRT pathway seems, in principle, compatible with antiviral development, given our increasingly nuanced understanding of the relative weakness and robustness of the host and viral processes.
doi:10.1111/j.1600-0854.2011.01208.x
PMCID: PMC3158961  PMID: 21518163
protein structure; virus budding; ALG-2; endosome; cytokinesis; ALIX; TSG101; UEV domain; WW domain; CEP55
18.  Functional architecture of the retromer cargo-recognition complex 
Nature  2007;449(7165):1063-1067.
The retromer complex 1, 2 is required for the sorting of acid hydrolases to lysosomes 3-7, transcytosis of the polymeric Ig receptor 8, Wnt gradient formation 9, 10, iron transporter recycling 11, and processing of the amyloid precursor protein 12. Human retromer consists of two smaller complexes, the cargo recognition Vps26:Vps29:Vps35 heterotrimer, and a membrane-targeting heterodimer or homodimer of SNX1 and/or SNX2 13. The crystal structure of a Vps29:Vps35 subcomplex shows how the metallophosphoesterase-fold subunit Vps29 14, 15 acts as a scaffold for the C-terminal half of Vps35. Vps35 forms a horseshoe-shaped right-handed α-helical solenoid whose concave face completely covers the metal-binding site of Vps29 and whose convex face exposes a series of hydrophobic interhelical grooves. Electron microscopy shows that the intact Vps26:Vps29:Vps35 complex is a stick-shaped, somewhat flexible, structure, ∼ 21 nm long. A hybrid structural model derived from crystal structures, electron microscopy, interaction studies, and bioinformatics shows that the α-solenoid fold extends the full length of Vps35, and that Vps26 is bound at the opposite end from Vps29. This extended structure presents multiple binding sites for the SNX complex and receptor cargo, and appears capable of flexing to conform to curved vesicular membranes.
doi:10.1038/nature06216
PMCID: PMC2377034  PMID: 17891154
19.  The retromer subunit Vps26 has an arrestin fold and binds Vps35 through its C-terminal domain 
The mammalian retromer complex consists of SNX1, SNX2, Vps26, Vps29, and Vps35, and retrieves lysosomal enzyme receptors from endosomes to the trans-Golgi network. The structure of human Vps26A at 2.1Å resolution reveals two curvedβ -sandwich domains connected by a polar core and a flexible linker. Vps26 has an unexpected structural relationship to arrestins. The Vps35-binding site on Vps26 maps to a mobile loop spanning residues 235–246, near the tip of the C-terminal domain. The loop is phylogenetically conserved and provides a mechanism for Vps26 integration into the complex that leaves the rest of the structure free for engagements with membranes and for conformational changes. Hydrophobic residues and a Gly in this loop are required for integration into the retromer complex and endosomal localization of human Vps26, and for the function of yeast Vps26 in carboxypeptidase Y sorting.
doi:10.1038/nsmb1103
PMCID: PMC1584284  PMID: 16732284
20.  Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5 
Rabex-5 is an exchange factor for Rab5, a master regulator of endosomal trafficking. Rabex-5 binds monoubiquitin, undergoes covalent ubiquitination, and contains an intrinsic ubiquitin E3 ligase activity, all of which require an N-terminal A20 zinc finger and an immediately C-terminal helix. The structure of the N-terminal portion of Rabex-5 bound to ubiquitin at 2.5 Å resolution shows that Rabex-5:ubiquitin interactions occur at two sites. The first site is a new type of ubiquitin binding domain, an inverted ubiquitin interaction motif (IUIM), that binds with ~29 μM affinity to the canonical Ile44 hydrophobic patch on ubiquitin. The second is a diaromatic patch on the A20 zinc finger, which binds with ~22 μM affinity to a polar region centered on Asp58 of ubiquitin. The A20 zinc finger diaromatic patch mediates E3 ligase activity by directly recruiting a ubiquitin-loaded ubiquitin conjugating enzyme.
doi:10.1038/nsmb1064
PMCID: PMC1578505  PMID: 16462746
21.  Nipped in the bud: How the AMSH MIT domain helps deubiquitinate lysosome-bound cargo 
Structure (London, England : 1993)  2011;19(8):1033-1035.
SUMMARY
Recruitment of the K63-linkage specific deubiquitinating enzyme AMSH is an important step in ESCRT-dependent membrane protein sorting. In this issue of Structure, Solomons et al. now reveal an extraordinarily high affinity complex between “MIM4” region of one ESCRT-III subunit, CHMP3, and the MIT domain of AMSH.
doi:10.1016/j.str.2011.07.002
PMCID: PMC3214632  PMID: 21827939
22.  Molecular Mechanisms of Ubiquitin-Dependent Membrane Traffic 
Annual Review of Biophysics  2011;40:119-142.
Over the past fourteen years, ubiquitination has emerged as a centrally important mechanism governing the subcellular trafficking of proteins. Ubiquitination, interaction with sorting factors that contain ubiquitin binding domains, and finally deubiquitination govern the itineraries of cargo proteins that include yeast carboxypeptidase S, the epithelial sodium channel ENaC, and epidermal growth factor receptor. The molecular structures and mechanisms of the paradigmatic HECT and RING domain ubiquitin ligases, JAMM and USP domain deubiquitinating enzymes, and numerous ubiquitin binding domains involved in these pathways, have been worked out in recent years and are described.
doi:10.1146/annurev-biophys-042910-155404
PMCID: PMC3272705  PMID: 21332354
Lysosome; vacuole; yeast genetics; EGF; EGF receptor; growth factor receptor; epithelial sodium channel; ENaC; yeast genetics; carboxypeptidase S; protein structure; crystal structure; ubiquitin; RING domain; HECT domain; JAMM domain; isopeptidase; ubiquitin ligase; deubiquitinating enzyme; ubiquitin binding domain; ESCRT complex
23.  Elucidation of New Binding Interactions with the Tumor Susceptibility Gene 101 (Tsg101) Protein Using Modified HIV-1 Gag-p6 Derived Peptide Ligands 
ACS medicinal chemistry letters  2011;2(5):337-341.
Targeting protein-protein interactions is gaining greater recognition as an attractive approach to therapeutic development. An example of this may be found with the human cellular protein encoded by the tumor susceptibility gene 101 (Tsg101), where interaction with the p6 C-terminal domain of the nascent viral Gag protein is required for HIV-1 particle budding and release. This association of Gag with Tsg101 is highly dependent on a “Pro-Thr-Ala-Pro” (“PTAP”) peptide sequence within the p6 protein. Although p6-derived peptides offer potential starting points for developing Tsg101-binding inhibitors, the affinities of canonical peptides are outside the useful range (Kd values greater than 50 μM). Reported herein are crystal structures of Tsg101 in complex with two structurally-modified PTAP-derived peptides. This data define new regions of ligand interaction not previously identified with canonical peptide sequences. This information could be highly useful in the design of Tsg101-binding antagonists.
doi:10.1021/ml1002579
PMCID: PMC3105896  PMID: 21643473
protein-protein interactions; Tsg101; X-ray crystal structure; peptide analogues
24.  Elucidation of New Binding Interactions with the Human Tsg101 Protein Using Modified HIV-1 Gag-p6 Derived Peptide Ligands 
ACS Medicinal Chemistry Letters  2011;2(5):337-341.
Targeting protein−protein interactions is gaining greater recognition as an attractive approach to therapeutic development. An example of this may be found with the human cellular protein encoded by the tumor susceptibility gene 101 (Tsg101), where interaction with the p6 C-terminal domain of the nascent viral Gag protein is required for HIV-1 particle budding and release. This association of Gag with Tsg101 is highly dependent on a “Pro-Thr-Ala-Pro” (“PTAP”) peptide sequence within the p6 protein. Although p6-derived peptides offer potential starting points for developing Tsg101-binding inhibitors, the affinities of canonical peptides are outside the useful range (Kd values greater than 50 μM). Reported herein are crystal structures of Tsg101 in complex with two structurally modified PTAP-derived peptides. These data define new regions of ligand interaction not previously identified with canonical peptide sequences. This information could be highly useful in the design of Tsg101-binding antagonists.
doi:10.1021/ml1002579
PMCID: PMC3105896  PMID: 21643473
Protein−protein interactions; Tsg101; X-ray crystal structure; peptide analogues
25.  Crystal Structure and Allosteric Activation of Protein Kinase C βII 
Cell  2011;144(1):55-66.
SUMMARY
Protein kinase C (PKC) isozymes are the paradigmatic effectors of lipid signaling. PKCs translocate to cell membranes and are allosterically activated upon binding of the lipid diacylglycerol to their C1A and C1B domains. The crystal structure of full-length protein kinase C βII was determined at 4.0 Å, revealing the conformation of an unexpected intermediate in the activation pathway. Here, the kinase active site is accessible to substrate, yet the conformation of the active site corresponds to a low-activity state because the ATP-binding side-chain of Phe629 of the conserved NFD motif is displaced. The C1B domain clamps the NFD helix in a low activity conformation, which is reversed upon membrane binding. A low resolution solution structure of the closed conformation of PKCβII was derived from small angle x-ray scattering. Together, these results show how PKCβII is allosterically in two steps, with the second step defining a novel protein kinase regulatory mechanism.
doi:10.1016/j.cell.2010.12.013
PMCID: PMC3104240  PMID: 21215369

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