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A Novel All Helix Fold of the AP180 Amino-Terminal Domain for Phosphoinositide Binding and Clathrin Assembly in Synaptic Vesicle Endocytosis

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A Novel All Helix Fold of the AP180 Amino-Terminal Domain for Phosphoinositide Binding and Clathrin Assembly in Synaptic Vesicle Endocytosis Cell, Vol. 104, 433±440, February 9, 2001, Copyright 2001 by Cell Press A Novel All Helix Fold of the AP180 Amino-Terminal Domain for Phosphoinositide Binding and Clathrin Assembly in Synaptic Vesicle Endocytosis Yuxin Mao,1 Jue Chen,2 Jennifer A. Maynard,4,6 Schmidt et al., 1999). Once coated vesicles are formed, Bing Zhang,5,6 and Florante A. Quiocho1,2,3,7 they are detached from the plasma membrane to enter 1Structural and Computational Biology and the cytoplasm by the dynamin GTPase-amphiphysin Molecular Biophysics Graduate Program complex (Koenig and Ikeda, 1989; Shupliakov et al., 2Howard Hughes Medical Institute 1997; Schmid et al., 1998). These endocytosed vesicles, 3Department of Biochemistry and Molecular Biology which only transiently retain their clathrin coats, then Baylor College of Medicine undergo a coat removal process so that they can be Houston, Texas 77030 reloaded with transmitters and poised for the next round 4Department of Chemical Engineering of exocytosis. Auxilin, hsc70, and the polyphosphoinosi- 5Section of Neurobiology, Institute for Neuroscience tide phosphatase synaptojanin have been proposed to 6Institute for Cellular and Molecular Biology assist in stripping the clathrin coats (Ungewickell et al., University of Texas 1995; Cremona et al., 1999). Austin, Texas 78712 Recently, the regulation of the assembly of clathrin- coated vesicles has received considerable attention. The clathrin assembly protein AP180 appears to be the Summary key player that determines the size of SVs by restricting the size of coated vesicles (Zhang et al., 1999). AP180 Clathrin-mediated endocytosis plays a major role in represents a growing family of monomeric clathrin as- retrieving synaptic vesicles from the plasma mem- sembly proteins that are widely distributed in a variety brane following exocytosis. This endocytic process of organisms (McMahon, 1999). Two isoforms of AP180 requires AP180 (or a homolog), which promotes the are found in yeast, but they do not seem to play a signifi- assembly and restricts the size of clathrin-coated vesi- cantly functional role in endocytosis (Wendland and cles. The highly conserved 33 kDa amino-terminal do- Emr, 1998; Huang et al., 1999). In mammals and humans, main of AP180 plays a critical role in binding to phos- two AP180 homologs are found to be either specifically phoinositides and in regulating the clathrin assembly present in presynaptic terminals (Ahle and Ungewickell, activity of AP180. The crystal structure of the amino- 1986; Sousa et al., 1992) or distributed ubiquitously terminal domain reported herein reveals a novel fold (Dreyling et al., 1996). Unlike in yeast, genetic deletion consisting of a large double layer of sheets of ten ␣ of AP180 homologs in Drosophila (LAP) (Zhang et al., helices and a unique site for binding phosphoinosi- 1998) and in C. elegans (UNC-11) (Nonet et al., 1999) tides. The finding that the clathrin-box motif is mostly significantly impairs SV endocytosis and alters the size buried and lies in a helix indicates a different site and of SVs in nerve terminals. Similarly, injection of interfer- mechanism for binding of the domain to clathrins than ing AP180 peptides into squid giant axons impairs syn- previously assumed. aptic transmission and alters SV size (Morgan et al., 1999). In vitro neuronal AP180 induces the formation Introduction of uniform sized clathrin cages (Ye and Lafer, 1995a), providing further evidence for the role of AP180 in regu- lating SV size. Synaptic transmission requires not only the release of At the primary structural level, the AP180s can be neurotransmitters through exocytosis of synaptic vesi- divided into two distinct domains, an amino- or N-termi- cles (SVs), but also the recycling of these vesicles nal domain and a carboxy- or C-terminal domain (Mur- (Heuser and Reese, 1973). At most synaptic terminals, phy et al., 1991; Morris et al., 1993; Ye and Lafer, 1995b). SV recycling is accomplished through clathrin-mediated The N-terminal domain (we named ªNAPº for N-terminal endocytosis that involves a series of sequential protein AP180 domain) of the AP180s contains about 300 highly and lipid interactions (Schmid, 1997; Zhang and Rama- conserved residues, whereas the C-terminal domain swami, 1999). The key steps of this endocytic process (to 600 residues 150ف) varies significantly both in length include assembly of clathrin-coated vesicles, pinching and similarity among all AP180 homologs (McMahon, off of these vesicles from the plasma membrane, and 1999). Despite the high degree of conservation and its removal of clathrin coats to release the nascent vesicles. interaction with clathrin triskelion, the NAP domain does Following exocytosis, clathrin triskelion and its assem- not assemble clathrin (Ye and Lafer, 1995b). Rather, the bly proteins (APs) AP-2 and AP180 initiate endocytosis NAP domain of AP180 appears to play a critical role in of SV components by assembling coated vesicles (Keen regulating the assembly activity of the AP180s, which et al., 1979; Gonzales-Gaitan and Jackle, 1997; Zhang is mediated by the C-terminal domain. The NAP domain et al., 1998; Morgan et al., 1999; Nonet et al., 1999). The shares three putative modules: a phosphoinositide bind- assembly of coats is further facilitated by endophilin, ing site (Norris et al., 1995; Hao et al., 1997), a clathrin a lysophosphatidic acid acyl transferase that assists binding site or ªclathrin-boxº motif (ter Haar et al., 2000), curvature formation by converting inverted cone-shaped and a leucine zipper (Wendland and Emr, 1998). AP180 lipids into cone-shaped lipids (Ringstad et al., 1999; binds both inositol (Norris et al., 1995) and phosphotidyl- inositol polyphosphates (Hao et al., 1997), which nega- 7 To whom correspondence should be addressed (e-mail: faq@bcm. tively regulate the activity of AP180 and inhibit clathrin tmc.edu). cage assembly. Binding to phosphoinositide moieties, Cell 434 Table 1. Crystallographic Analysis Statistics A. Data Collection No. of Unique Ê Ê a,b Crystal Wavelength (A)dmin (A) Measurements Reflections Completeness (%) ϽIϾ/Ͻ␴Ͼ Rsym (%) MAD Phasing data SeMet ␭1 (0.9793) 2.3 244,157 66,748 99.4 (100) 25.0 (5.5) 6.3 (23.1) SeMet ␭2 (0.9788) 2.3 246,217 67,191 99.5 (100) 24.0 (4.4) 6.4 (27.1) SeMet ␭3 (0.9712) 2.3 248,253 67,292 99.7 (100) 22.9 (3.5) 6.2 (30.1) Refinement data SeMet ␭1 (0.9793) 2.2 274,148 38,772 99.6 (100) 33.0 (5.4) 7.6 (33.7) B. Phasing Observed Diffraction Ratiosc ␭1 ␭2 ␭3 ␭1 0.0677 0.0440 0.0578 ␭2 0.0844 0.0462 ␭3 0.0661 Figure of Merit (FOM) before/after solvent flattening 0.64/0.95 C. Refinement Bonded Main Bonded Side Chain Resolution Bond Length Bond Angle Chain Atom B Atom B Factor range (AÊ ) R valued (%) R freee (%) Deviation (AÊ ) Deviation (Њ) Factor rmsd (AÊ 2) rmsd (AÊ 2) 50±2.2 21.1 25.3 0.012 1.3 4.15 2.32 a Values in parentheses are for the outer resolution shell. b Rsym ϭ ͚h͚i͉II(h) ϪϽI(h)͉/͚h͚iII(h). c Values are Ͻ(⌬͉F͉)2Ͼ1¤2/Ͻ͉F͉2Ͼ1¤2. d R value ϭ ͚(͉Fobs͉ Ϫ k ͉Fcal͉)/͚͉Fobs͉. e R free is obtained for a test set of reflections, consisting of a randomly selected 5% of the data and not used during refinement. as well as to clathrins, may also promote membrane (MAD) phasing technique (Experimental Procedures and association and proper localization of clathrin near the Table 1). The structure, missing the first eighteen disor- plasma membrane (Zhang et al., 1998). dered residues, is composed entirely of ten ␣ helices The clathrin-box motif, with the canonical sequence and connecting loops, all of varying lengths (Figure 1). L(L,I)(D,E,N)(L,F)(D,E), occurs in several proteins, includ- The helices are folded roughly into a large triangular- ing AP180s, that are involved in the clathrin coat assem- shaped layer of two sheets of about 20 AÊ thick. The bly process and endocytosis (Dell'Angelica et al., 1998; large sheet made up of helices ␣1, ␣3, ␣6, ␣7, ␣9, and ter Haar et al., 2000). The clathrin box of some of these ␣10 dominates the structure. The smaller sheet is com- proteins (e.g., nonvisual arrestins, ␤3 subunit of AP-3 posed of helices ␣2, ␣4, and ␣8. Many hydrophobic and epsin) has been demonstrated to bind to the N-termi- residues occupy the space between the two sheets of nal domain (td40) of clathrin heavy chain (Goodman et helices. Although the entire domain is compact, two al., 1997; Dell'Angelica et al., 1998; Drake et al., 2000). different packing arrangements of the ␣ helices are evi- Moreover, recent crystal structure determination of the dent (Figure 1). The first four short helices, which consti- td40 complexed with short peptides containing the tute less than a third of the entire domain, fold into two clathrin-box motif from ␤-arrestin 2 and AP-3 revealed two-helix hairpins (␣1 and ␣2 and ␣3 and ␣4). These two an extended peptide conformation with the motif bound helix hairpins are similar to the HEAT repeat that is the in the groove between blades 1 and 2 of the ␤ propeller building unit of several large superhelix-of-helices struc- structure of the td40 (ter Haar et al., 2000). tures of a variety of domains, proteins, and enzymes To define the atomic structure and gain molecular (Groves and Barford, 1999). The last five long helices, insights into the roles of the conserved motifs in AP180± which constitute the bulk of the NAP domain, form a clathrin interactions, we have determined the 2.2 AÊ crys- slightly twisted sheet of four helices (␣6, ␣7, ␣9, and tal structure of the recombinant NAP domain of LAP by ␣10) with the longest helix of the domain (␣8) packed X-ray crystallography.
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