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1Tt5 Lichtarge Lab 2006 Pages 1–21 1tt5 Evolutionary trace report by report maker January 22, 2010 4 Notes on using trace results 19 4.1 Coverage 19 4.2 Known substitutions 19 4.3 Surface 19 4.4 Number of contacts 19 4.5 Annotation 19 4.6 Mutation suggestions 19 5 Appendix 19 5.1 File formats 19 5.2 Color schemes used 19 5.3 Credits 20 5.3.1 Alistat 20 5.3.2 CE 20 5.3.3 DSSP 20 5.3.4 HSSP 20 5.3.5 LaTex 20 5.3.6 Muscle 20 5.3.7 Pymol 20 5.4 Note about ET Viewer 20 5.5 Citing this work 20 CONTENTS 5.6 About report maker 20 5.7 Attachments 20 1 Introduction 1 2 Chain 1tt5A 1 1 INTRODUCTION 2.1 Q13564 overview 1 From the original Protein Data Bank entry (PDB id 1tt5): 2.2 Multiple sequence alignment for 1tt5A 1 Title: Structure of appbp1-uba3-ubc12n26: a unique e1-e2 interac- 2.3 Residue ranking in 1tt5A 2 tion required for optimal conjugation of the ubiquitin-like protein 2.4 Top ranking residues in 1tt5A and their position on nedd8 the structure 2 Compound: Mol id: 1; molecule: amyloid protein-binding pro- 2.4.1 Clustering of residues at 25% coverage. 2 tein 1; chain: a, c; synonym: appbp1; engineered: yes; mol id: 2; 2.4.2 Overlap with known functional surfaces at molecule: ubiquitin-activating enzyme e1c isoform 1; chain: b, d; 25% coverage. 3 fragment: residues 33-463; synonym: uba3, nedd8-activating enzyme 2.4.3 Possible novel functional surfaces at 25% huba3; engineered: yes; mol id: 3; molecule: ubiquitin-conjugating coverage. 6 enzyme e2 m; chain: e, f; fragment: residues 1-26; synonym: ubc12n26, ubiquitin-protein ligase m, ubiquitin carrier protein m, 3 Chain 1tt5B 9 nedd8-conjugating enzyme ubc12; engineered: yes 3.1 Q8TBC4 overview 9 Organism, scientific name: Homo Sapiens; 3.2 Multiple sequence alignment for 1tt5B 10 1tt5 contains unique chains 1tt5A (522 residues) and 1tt5B (414 3.3 Residue ranking in 1tt5B 10 residues) 1tt5C is a homologue of chain 1tt5A. 1tt5D is a homo- 3.4 Top ranking residues in 1tt5B and their position on logue of chain 1tt5B. Chains 1tt5E and 1tt5F are too short to permit the structure 10 statistically significant analysis, and were treated as a peptide ligands. 3.4.1 Clustering of residues at 25% coverage. 10 3.4.2 Overlap with known functional surfaces at 2 CHAIN 1TT5A 25% coverage. 11 3.4.3 Possible novel functional surfaces at 25% 2.1 Q13564 overview coverage. 16 From SwissProt, id Q13564, 97% identical to 1tt5A: 1 Lichtarge lab 2006 Description: Amyloid protein-binding protein 1 (Amyloid beta pre- cursor protein- binding protein 1, 59 kDa) (APP-BP1) (Protoonco- gene protein 1) (HPP1). Organism, scientific name: Homo sapiens (Human). Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. Function: The dimeric enzyme activates NEDD8 by first adenylating its C-terminal glycine residue with ATP and thereafter linking this residue to the side chain of a cysteine residue on UBE1C, yielding a NEDD8-UBE1C thiolester and free AMP. Necessary for cell cycle progression through the S-M checkpoint. Overexpression of APPBP1 causes apoptosis through deregulation of NEDD8 conjugation. Enzyme regulation: Binding of TP53BP2 to the regulatory subunit APPBP1 decreases neddylation activity. Pathway: NEDD8 conjugation; first step. Subunit: Heterodimer of UBE1C and APPBP1. The complex binds Fig. 1. Residues 1-273 in 1tt5A colored by their relative importance. (See NEDD8. Binds APP and TP53BP2. Appendix, Fig.17, for the coloring scheme.) Subcellular location: Colocalizes with APP in lipid rafts. Tissue specificity: Ubiquitous in fetal tissues. Expressed throughout the adult brain. Miscellaneous: APPBP1 and UBE1C correspond to the N-terminal and the C-terminal part of yeast UBA3. In yeast the two subunits form a single polypeptide chain. Similarity: Belongs to the ubiquitin-activating E1 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 and this statement is not removed. 2.2 Multiple sequence alignment for 1tt5A For the chain 1tt5A, the alignment 1tt5A.msf (attached) with 81 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as Fig. 2. Residues 274-534 in 1tt5A colored by their relative importance. (See duplicate sequences were removed. It can be found in the attachment Appendix, Fig.17, for the coloring scheme.) to this report, under the name of 1tt5A.msf. Its statistics, from the alistat program are the following: 2.3 Residue ranking in 1tt5A Format: MSF The 1tt5A sequence is shown in Figs. 1–2, with each residue colored Number of sequences: 81 according to its estimated importance. The full listing of residues Total number of residues: 34273 in 1tt5A can be found in the file called 1tt5A.ranks sorted in the Smallest: 149 attachment. Largest: 522 Average length: 423.1 2.4 Top ranking residues in 1tt5A and their position on Alignment length: 522 the structure Average identity: 34% In the following we consider residues ranking among top 25% of resi- Most related pair: 99% dues in the protein . Figure 3 shows residues in 1tt5A colored by their Most unrelated pair: 6% importance: bright red and yellow indicate more conserved/important Most distant seq: 35% residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Furthermore, <1% of residues show as conserved in this ali- 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the gnment. top 25% of all residues, this time colored according to clusters they The alignment consists of 23% eukaryotic ( 7% vertebrata, 1% belong to. The clusters in Fig.4 are composed of the residues listed arthropoda, 9% fungi, 4% plantae) sequences. (Descriptions of in Table 1. some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1tt5A.descr. 2 Table 1. continued cluster size member color residues red 56 184,188,192,209,210,211,212 213,214,217,218,220,222,225 261,262,263,264,265,267,268 271,272,274,304,305,308,310 311,312,314,323,324,325,326 327,330,331,332,334,336,339 342,343,346,349,350,353,380 383,384,385,386,387,390,392 blue 51 9,12,13,14,15,16,17,18,19,20 21,24,25,28,31,42,44,46,47 48,49,51,52,53,55,57,93,95 96,97,100,155,157,158,160 489,491,493,498,499,501,502 503,504,506,507,510,512,513 515,522 yellow 5 69,71,73,74,76 green 3 37,61,86 purple 2 34,123 azure 2 234,240 Fig. 3. Residues in 1tt5A, colored by their relative importance. Clockwise: turquoise 2 518,519 front, back, top and bottom views. brown 2 481,484 Table 1. Clusters of top ranking residues in 1tt5A. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Interface with 1tt5B.Table 2 lists the top 25% of residues at the interface with 1tt5B. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 4.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 157 G G(100) 0.00 3/3 4.35 504 E .(24) 0.01 12/0 3.21 E(75) 507 K .(24) 0.01 27/0 2.58 K(75) 331 D .(25) 0.02 34/1 2.58 D(74) 47 K K(96) 0.03 29/0 3.12 S(1) .(2) Fig. 4. Residues in 1tt5A, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for 484 R .(25) 0.03 108/17 2.68 the coloring scheme). Clockwise: front, back, top and bottom views. The R(71) corresponding Pymol script is attached. S(2) 44 E E(92) 0.04 14/0 3.20 R(1) Table 1. .(2) cluster size member Q(2) color residues continued in next column continued in next column 3 Table 2. continued Table 2. continued res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) X(1) F(1) 332 M .(25) 0.04 15/15 3.14 .(2) M(71) 334 A .(25) 0.09 26/26 3.30 I(1) A(45) F(1) S(24) 499 G .(25) 0.04 24/24 3.28 T(1) G(72) C(2) S(1) 336 S .(25) 0.09 46/15 2.48 51 L L(95) 0.05 45/12 3.02 S(39) .(2) T(34) I(1) 343 Q .(25) 0.09 2/0 4.73 F(1) Q(66) 96 L L(95) 0.05 7/1 3.92 A(3) F(2) P(1) M(2) K(1) 481 E .(25) 0.06 39/4 2.80 R(1) E(71) 491 H .(25) 0.09 44/0 2.82 D(1) H(69) S(1) N(1) 13 Y Y(92) 0.07 9/4 3.93 P(2) .(6) Q(1) K(1) 19 L V(23) 0.11 37/1 3.50 15 R R(92) 0.07 98/28 2.86 L(55) .(6) I(14) N(1) .(4) 16 Q Q(92) 0.07 32/9 2.99 X(1) .(6) 95 E E(91) 0.11 33/14 2.96 E(1) Q(2) 18 R Y(23) 0.07 61/5 2.99 .(2) R(70) A(1) .(4) R(1) X(1) D(1) 20 W L(23) 0.07 11/0 3.80 339 Y .(25) 0.11 27/0 3.37 W(70) Y(65) .(4) F(7) X(1) R(1) 211 H .(24) 0.07 14/1 3.77 12 K L(23) 0.12 39/28 3.45 H(64) K(56) K(8) R(12) E(1) .(6) Q(1) T(1) 503 Q .(24) 0.07 41/5 3.21 73 N Q(23) 0.12 7/7 4.22 Q(70) N(69) H(3) .(4) L(1) T(1) 14 D S(23) 0.08 8/0 3.81 R(1) D(69) 489 E .(25) 0.12 26/19 2.65 .(6) E(64) T(1) H(1) 48 N N(83) 0.08 26/3 3.85 Q(2) S(3) S(2) G(8) K(1) continued in next column continued in next column 4 Table 2.
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