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1Luj Lichtarge Lab 2006 Pages 1–11 1luj Evolutionary trace report by report maker October 1, 2010 4 Notes on using trace results 9 4.1 Coverage 9 4.2 Known substitutions 9 4.3 Surface 9 4.4 Number of contacts 9 4.5 Annotation 9 4.6 Mutation suggestions 9 5 Appendix 9 5.1 File formats 9 5.2 Color schemes used 9 5.3 Credits 10 5.3.1 Alistat 10 5.3.2 CE 10 5.3.3 DSSP 10 5.3.4 HSSP 10 5.3.5 LaTex 10 5.3.6 Muscle 10 5.3.7 Pymol 10 5.4 Note about ET Viewer 10 5.5 Citing this work 10 5.6 About report maker 10 CONTENTS 5.7 Attachments 10 1 Introduction 1 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1luj): 2 Chain 1lujA 1 Title: Crystal structure of the beta-catenin/icat complex 2.1 Q5R2I4 overview 1 Compound: Mol id: 1; molecule: beta-catenin; chain: a; fragment: 2.2 Multiple sequence alignment for 1lujA 1 residues 150-666; engineered: yes; mol id: 2; molecule: beta-catenin- 2.3 Residue ranking in 1lujA 1 interacting protein icat; chain: b; engineered: yes 2.4 Top ranking residues in 1lujA and their position on Organism, scientific name: Homo Sapiens; the structure 1 1luj contains unique chains 1lujA (501 residues) and 1lujB (71 2.4.1 Clustering of residues at 25% coverage. 2 residues) 2.4.2 Overlap with known functional surfaces at 25% coverage. 2 2 CHAIN 1LUJA 2.4.3 Possible novel functional surfaces at 25% coverage. 4 2.1 Q5R2I4 overview From SwissProt, id Q5R2I4, 94% identical to 1lujA: 3 Chain 1lujB 6 Description: Beta-catenin homologue. 3.1 Q9JJN6 overview 6 Organism, scientific name: Trionyx sinensis (Chinese softshell 3.2 Multiple sequence alignment for 1lujB 6 turtle) (Pelodiscus sinensis). 3.3 Residue ranking in 1lujB 6 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 3.4 Top ranking residues in 1lujB and their position on Euteleostomi; Testudines; Cryptodira; Trionychoidea; Trionychidae; the structure 7 Pelodiscus. 3.4.1 Clustering of residues at 25% coverage. 7 3.4.2 Overlap with known functional surfaces at 2.2 Multiple sequence alignment for 1lujA 25% coverage. 7 For the chain 1lujA, the alignment 1lujA.msf (attached) with 36 3.4.3 Possible novel functional surfaces at 25% sequences was used. The alignment was downloaded from the HSSP coverage. 8 database, and fragments shorter than 75% of the query as well as 1 Lichtarge lab 2006 Fig. 1. Residues 150-399 in 1lujA colored by their relative importance. (See Appendix, Fig.13, for the coloring scheme.) Fig. 2. Residues 400-663 in 1lujA colored by their relative importance. (See duplicate sequences were removed. It can be found in the attachment Appendix, Fig.13, for the coloring scheme.) to this report, under the name of 1lujA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 36 Total number of residues: 17648 Smallest: 392 Largest: 501 Average length: 490.2 Alignment length: 501 Average identity: 58% Most related pair: 99% Most unrelated pair: 20% Most distant seq: 40% Furthermore, 4% of residues show as conserved in this alignment. The alignment consists of 55% eukaryotic ( 19% vertebrata, 11% arthropoda) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1lujA.descr. 2.3 Residue ranking in 1lujA The 1lujA sequence is shown in Figs. 1–2, with each residue colored Fig. 3. Residues in 1lujA, colored by their relative importance. Clockwise: according to its estimated importance. The full listing of residues front, back, top and bottom views. in 1lujA can be found in the file called 1lujA.ranks sorted in the attachment. Table 1. 2.4 Top ranking residues in 1lujA and their position on cluster size member the structure color residues In the following we consider residues ranking among top 25% of resi- red 89 216,219,222,240,244,254,255 dues in the protein . Figure 3 shows residues in 1lujA colored by their 257,258,259,260,261,262,270 importance: bright red and yellow indicate more conserved/important 286,290,292,294,296,299,301 residues (see Appendix for the coloring scheme). A Pymol script for 304,312,315,316,320,321,324 producing this figure can be found in the attachment. 325,328,333,334,335,336,338 339,342,343,344,345,347,348 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the 349,350,353,354,358,361,366 top 25% of all residues, this time colored according to clusters they 374,376,377,380,382,383,386 belong to. The clusters in Fig.4 are composed of the residues listed continued in next column in Table 1. 2 Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 386 R R(100) 0.04 42/12 3.31 387 N N(100) 0.04 23/7 3.13 389 S S(100) 0.04 3/1 4.57 390 D D(100) 0.04 31/9 3.34 426 N N(100) 0.04 41/3 2.68 435 K K(100) 0.04 6/0 2.67 469 R R(100) 0.04 30/2 2.76 470 H H(100) 0.04 51/11 2.91 516 N N(91) 0.06 1/0 4.78 K(8) 345 K K(91) 0.08 29/4 3.21 R(8) 425 S S(94) 0.08 1/1 4.97 C(5) 430 N N(94) 0.08 23/5 2.95 G(5) 349 V V(88) 0.10 26/0 3.24 I(2) .(8) Fig. 4. Residues in 1lujA, colored according to the cluster they belong to: 612 R R(88) 0.10 22/0 2.99 red, followed by blue and yellow are the largest clusters (see Appendix for C(2) the coloring scheme). Clockwise: front, back, top and bottom views. The .(8) corresponding Pymol script is attached. 654 Y Y(88) 0.10 29/0 2.79 F(2) .(8) Table 1. continued 429 C C(86) 0.11 30/6 2.92 cluster size member A(8) color residues S(5) 387,388,389,390,418,419,422 578 H H(86) 0.11 12/0 3.96 425,426,427,428,429,430,431 .(8) 434,435,443,447,462,463,466 Q(5) 467,468,469,470,472,474,475 312 K K(97) 0.13 7/0 2.74 513,515,516,519,520 R(2) blue 24 508,563,564,566,569,571,572 620 E E(83) 0.13 14/0 2.69 576,577,578,612,613,616,617 Q(8) 618,620,621,640,653,654,655 .(8) 657,658,659 422 G G(94) 0.14 7/7 3.94 yellow 3 227,231,232 Q(5) green 2 401,405 474 R R(83) 0.14 37/0 2.92 purple 2 539,540 K(2) azure 2 625,628 G(8) N(5) Table 1. Clusters of top ranking residues in 1lujA. 653 T T(86) 0.15 30/6 3.10 A(5) .(8) 2.4.2 Overlap with known functional surfaces at 25% coverage. 428 T T(91) 0.17 3/3 4.08 The name of the ligand is composed of the source PDB identifier L(2) and the heteroatom name used in that file. V(5) Interface with 1lujB.Table 2 lists the top 25% of residues at the 515 R R(91) 0.17 40/0 2.64 interface with 1lujB. The following table (Table 3) suggests possible continued in next column disruptive replacements for these residues (see Section 4.6). 3 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) N(2) L(5) 613 V V(77) 0.19 1/0 4.38 E(8) .(8) A(5) 657 A A(75) 0.22 7/3 3.85 G(8) S(2) .(8) I(5) Table 2. The top 25% of residues in 1lujA at the interface with 1lujB. (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 number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Fig. 5. Residues in 1lujA, at the interface with 1lujB, colored by their relative Table 3. importance. 1lujB is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 1lujA.) res type disruptive mutations 386 R (TD)(SYEVCLAPIG)(FMW)(N) 2.4.3 Possible novel functional surfaces at 25% coverage. One 387 N (Y)(FTWH)(SEVCARG)(MD) group of residues is conserved on the 1lujA surface, away from (or 389 S (KR)(FQMWH)(NYELPI)(D) susbtantially larger than) other functional sites and interfaces reco- 390 D (R)(FWH)(KYVCAG)(TQM) gnizable in PDB entry 1luj. It is shown in Fig. 6. The right panel 426 N (Y)(FTWH)(SEVCARG)(MD) shows (in blue) the rest of the larger cluster this surface belongs to. 435 K (Y)(FTW)(SVCAG)(HD) 469 R (TD)(SYEVCLAPIG)(FMW)(N) 470 H (E)(TQMD)(SNKVCLAPIG)(YR) 516 N (Y)(FTW)(H)(SVCAG) 345 K (Y)(T)(FW)(SVCAG) 425 S (KR)(FQMWH)(E)(NYLPI) 430 N (Y)(FWH)(ER)(T) 349 V (Y)(R)(KE)(H) 612 R (D)(ELPI)(T)(VA) 654 Y (K)(Q)(M)(E) 429 C (KR)(E)(QH)(FMW) 578 H (E)(T)(D)(VMCAG) 312 K (Y)(T)(FW)(SVCAG) 620 E (FWH)(YVCAG)(TR)(S) 422 G (FEWHR)(KYD)(M)(QLPI) Fig.
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