Pages 1–9 2vj0 Evolutionary trace report by report maker June 1, 2010 4.3.1 Alistat 9 4.3.2 CE 9 4.3.3 DSSP 9 4.3.4 HSSP 9 4.3.5 LaTex 9 4.3.6 Muscle 9 4.3.7 Pymol 9 4.4 Note about ET Viewer 9 4.5 Citing this work 9 4.6 About report maker 9 4.7 Attachments 9 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2vj0): Title: Crystal structure of the alpha-adaptin appendage domain, from the ap2 adaptor complex, in complex with an fxdnf peptide from amphiphysin1 and a wvxf peptide from synaptojanin p170 Compound: Mol id: 1; molecule: ap-2 complex subunit alpha-2; synonym: adapter-related protein complex 2 alpha-2 subunit, alpha- adaptin c, adaptor protein complex ap-2 alpha-2 subunit, clathrin CONTENTS assembly protein complex 2 alpha-c large chain, 100 kda coated vesicle protein c, plasma membrane adaptor ha2/ap2 adaptin alpha 1 Introduction 1 c subunit; chain: a; fragment: appendage domain, residues 693-938; engineered: yes; mol id: 2; molecule: synaptojanin-1; synonym: 2 Chain 2vj0A 1 synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1,synaptojanin-1 2.1 P18484 overview 1 p170; chain: p; fragment: peptide containing wvxf motif, residues 2.2 Multiple sequence alignment for 2vj0A 1 1479-1490; mol id: 3; molecule: amphiphysin; synonym: amphiphy- 2.3 Residue ranking in 2vj0A 2 sin1; chain: q; fragment: peptide containing fxdnf motif, residues 2.4 Top ranking residues in 2vj0A and their position on 324-330 the structure 2 Organism, scientific name: Rattus Norvegicus; 2.4.1 Clustering of residues at 25% coverage. 2 2vj0 contains a single unique chain 2vj0A (246 residues long). 2.4.2 Overlap with known functional surfaces at Chains 2vj0P and 2vj0Q are too short to permit statistically signi- 25% coverage. 3 ficant analysis, and were treated as a peptide ligands. 2.4.3 Possible novel functional surfaces at 25% coverage. 5 2 CHAIN 2VJ0A 3 Notes on using trace results 7 3.1 Coverage 7 2.1 P18484 overview 3.2 Known substitutions 8 From SwissProt, id P18484, 99% identical to 2vj0A: 3.3 Surface 8 Description: Adapter-related protein complex 2 alpha 2 subunit 3.4 Number of contacts 8 (Alpha-adaptin C) (Adaptor protein complex AP-2 alpha-2 subu- 3.5 Annotation 8 nit) (Clathrin assembly protein complex 2 alpha-C large chain) (100 3.6 Mutation suggestions 8 kDa coated vesicle protein C) (Plasma membrane adaptor HA2/AP2 adaptin alpha C subunit). 4 Appendix 8 Organism, scientific name: Rattus norvegicus (Rat). 4.1 File formats 8 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Verte- 4.2 Color schemes used 8 brata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; 4.3 Credits 9 Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Rattus. 1 Lichtarge lab 2006 Function: Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated pro- tein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Alpha adaptin is a subunit of the plasma membrane adaptor. Binds polyphosphoinositide-containing lipids. Subunit: Adaptor protein complex 2 (AP-2) is an heterote- tramer composed of two large adaptins (alpha1A/AP2A1 or alpha1B/AP2A1 or alpha2/AP2A2 and beta1/AP2B1), a medium Fig. 1. Residues 693-815 in 2vj0A colored by their relative importance. (See adaptin (mu2/AP2M1) and a small adaptin (sigma2long/AP2S1 or Appendix, Fig.12, for the coloring scheme.) sigma2short/AP2S1). Binds EPN1, EPS15, AMPH, SNAP91 and BIN1 (By similarity). Interaction: Subcellular location: Component of the coat surrounding the cyto- plasmic face of coated vesicles in the plasma membrane. Tissue specificity: Widely expressed. Similarity: Belongs to the adaptor complexes large subunit family. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified Fig. 2. Residues 816-938 in 2vj0A colored by their relative importance. (See and this statement is not removed. Appendix, Fig.12, for the coloring scheme.) 2.4 Top ranking residues in 2vj0A and their position on 2.2 Multiple sequence alignment for 2vj0A the structure For the chain 2vj0A, the alignment 2vj0A.msf (attached) with 47 In the following we consider residues ranking among top 25% of resi- sequences was used. The alignment was downloaded from the HSSP dues in the protein . Figure 3 shows residues in 2vj0A colored by their database, and fragments shorter than 75% of the query as well as importance: bright red and yellow indicate more conserved/important duplicate sequences were removed. It can be found in the attachment residues (see Appendix for the coloring scheme). A Pymol script for to this report, under the name of 2vj0A.msf. Its statistics, from the producing this figure can be found in the attachment. alistat program are the following: Format: MSF Number of sequences: 47 Total number of residues: 11295 Smallest: 219 Largest: 246 Average length: 240.3 Alignment length: 246 Average identity: 42% Most related pair: 98% Most unrelated pair: 22% Most distant seq: 37% Furthermore, 5% of residues show as conserved in this alignment. The alignment consists of 27% eukaryotic ( 17% vertebrata, 8% fungi) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 2vj0A.descr. 2.3 Residue ranking in 2vj0A The 2vj0A sequence is shown in Figs. 1–2, with each residue colored Fig. 3. Residues in 2vj0A, colored by their relative importance. Clockwise: according to its estimated importance. The full listing of residues front, back, top and bottom views. in 2vj0A can be found in the file called 2vj0A.ranks sorted in the attachment. 2 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Table 2. top 25% of all residues, this time colored according to clusters they res type subst’s cvg noc/ dist antn belong to. The clusters in Fig.4 are composed of the residues listed (%) bb (A˚ ) 729 E R(4) 0.09 14/10 3.44 site E(95) 735 G G(85) 0.15 10/10 3.67 site A(14) 731 R Q(6) 0.16 7/5 3.96 R(82) K(2) T(2) H(6) Table 2. The top 25% of residues in 2vj0A at the interface with dithiane diol.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 3. res type disruptive mutations 729 E (FW)(YVCAHG)(T)(SLPIR) 735 G (KER)(QHD)(FYMW)(N) 731 R (TD)(Y)(E)(VA) Fig. 4. Residues in 2vj0A, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for Table 3. List of disruptive mutations for the top 25% of residues in 2vj0A, the coloring scheme). Clockwise: front, back, top and bottom views. The that are at the interface with dithiane diol. corresponding Pymol script is attached. Figure 5 shows residues in 2vj0A colored by their importance, at the in Table 1. interface with 2vj0ADTD1940. Sulfate ion binding site. Table 4 lists the top 25% of residues at Table 1. the interface with 2vj0ASO41943 (sulfate ion). The following table cluster size member (Table 5) suggests possible disruptive replacements for these residues color residues (see Section 3.6). red 53 708,714,715,716,717,718,719 722,723,724,725,740,743,744 Table 4. 782,784,785,795,799,818,819 res type subst’s cvg noc/ dist 823,824,825,831,836,837,839 (%) bb (A˚ ) 840,843,849,851,871,872,880 728 S S(76) 0.21 1/1 4.85 881,882,883,886,888,891,892 T(6) 901,902,903,905,906,907,908 L(6) 909,916,918,920 A(10) blue 4 727,728,729,735 yellow 3 752,805,812 Table 4. The top 25% of residues in 2vj0A at the interface with sulfate ion.(Field names: res: residue number in the PDB entry; type: amino acid Table 1. Clusters of top ranking residues in 2vj0A. type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: 2.4.2 Overlap with known functional surfaces at 25% coverage. distance of closest apporach to the ligand. ) The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Dithiane diol binding site. Table 2 lists the top 25% of residues at the interface with 2vj0ADTD1940 (dithiane diol). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). 3 Fig. 5. Residues in 2vj0A, at the interface with dithiane diol, colored by their Fig. 6. Residues in 2vj0A, at the interface with sulfate ion, colored by their relative importance. The ligand (dithiane diol) is colored green. Atoms further relative importance. The ligand (sulfate ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed.