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1Yz4 Lichtarge Lab 2006 Pages 1–7 1yz4 Evolutionary trace report by report maker September 26, 2008 4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 7 4.4 Note about ET Viewer 7 4.5 Citing this work 7 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1yz4): Title: Crystal structure of dusp15 Compound: Mol id: 1; molecule: dual specificity phosphatase-like CONTENTS 15 isoform a; chain: a, b; fragment: catalytic domain; synonym: dusp15; ec: 3.1.3.48; engineered: yes; mutation: yes 1 Introduction 1 Organism, scientific name: Homo Sapiens; 1yz4 contains a single unique chain 1yz4A (159 residues long) and 2 Chain 1yz4A 1 its homologue 1yz4B. 2.1 Q6PGN7 overview 1 2.2 Multiple sequence alignment for 1yz4A 1 2.3 Residue ranking in 1yz4A 1 2.4 Top ranking residues in 1yz4A and their position on the structure 1 2 CHAIN 1YZ4A 2.4.1 Clustering of residues at 25% coverage. 1 2.1 Q6PGN7 overview 2.4.2 Overlap with known functional surfaces at 25% coverage. 2 From SwissProt, id Q6PGN7, 99% identical to 1yz4A: 2.4.3 Possible novel functional surfaces at 25% Description: Dual specificity phosphatase 15, isoform a. coverage. 4 Organism, scientific name: Homo sapiens (Human). Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 3 Notes on using trace results 5 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; 3.1 Coverage 5 Catarrhini; Hominidae; Homo. 3.2 Known substitutions 6 3.3 Surface 6 3.4 Number of contacts 6 2.2 Multiple sequence alignment for 1yz4A 3.5 Annotation 6 3.6 Mutation suggestions 6 For the chain 1yz4A, the alignment 1yz4A.msf (attached) with 58 sequences was used. The alignment was assembled through combi- 4 Appendix 6 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 6 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 6 report, under the name of 1yz4A.msf. Its statistics, from the alistat 4.3 Credits 7 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues -2-156 in 1yz4A colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Format: MSF Number of sequences: 58 Total number of residues: 8870 Smallest: 121 Largest: 159 Average length: 152.9 Alignment length: 159 Average identity: 35% Most related pair: 98% Fig. 2. Residues in 1yz4A, colored by their relative importance. Clockwise: Most unrelated pair: 21% front, back, top and bottom views. Most distant seq: 35% Furthermore, 3% of residues show as conserved in this alignment. The alignment consists of 96% eukaryotic ( 62% vertebrata, 12% arthropoda, 1% fungi, 3% plantae), and 1% viral sequences. (Des- criptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1yz4A.descr. 2.3 Residue ranking in 1yz4A The 1yz4A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1yz4A can be found in the file called 1yz4A.ranks sorted in the attachment. 2.4 Top ranking residues in 1yz4A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 1yz4A colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 3. Residues in 1yz4A, colored according to the cluster they belong to: 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the red, followed by blue and yellow are the largest clusters (see Appendix for top 25% of all residues, this time colored according to clusters they the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Table 1. Table 1. continued cluster size member cluster size member color residues color residues 36,37,50,57,67,73,74,85,86 red 39 8,12,13,14,15,20,26,31,33,34 87,88,90,91,93,94,95,97,101 continued in next column 102,104,114,118,122,127,128 continued in next column 2 Table 1. continued cluster size member color residues 130,131,134,135 Table 1. Clusters of top ranking residues in 1yz4A. 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. B-octylglucoside binding site. Table 2 lists the top 25% of resi- dues at the interface with 1yz4BOG210 (b-octylglucoside). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 94 R R(100) 0.03 10/0 3.06 90 A A(74) 0.17 3/2 4.17 V(6) F(3) Fig. 4. Residues in 1yz4A, at the interface with b-octylglucoside, colored M(13) by their relative importance. The ligand (b-octylglucoside) is colored green. C(1) Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the Table 2. The top 25% of residues in 1yz4A at the interface with b- coloring scheme for the protein chain 1yz4A.) octylglucoside.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percen- tage of each type in the bracket; noc/bb: number of contacts with the ligand, Table 4. continued with the number of contacts realized through backbone atoms given in the res type subst’s cvg noc/ dist bracket; dist: distance of closest apporach to the ligand. ) (%) bb (A˚ ) 95 S S(96) 0.04 3/2 4.52 A(3) Table 3. 88 S C(93) 0.07 22/12 2.50 res type disruptive S(1) mutations G(5) 94 R (TD)(SYEVCLAPIG)(FMW)(N) 90 A A(74) 0.17 18/14 2.84 90 A (KER)(Y)(D)(Q) V(6) F(3) Table 3. List of disruptive mutations for the top 25% of residues in M(13) 1yz4A, that are at the interface with b-octylglucoside. C(1) Figure 4 shows residues in 1yz4A colored by their importance, at the Table 4. The top 25% of residues in 1yz4A at the interface with sulfate interface with 1yz4BOG210. ion.(Field names: res: residue number in the PDB entry; type: amino acid Sulfate ion binding site. Table 4 lists the top 25% of residues type; substs: substitutions seen in the alignment; with the percentage of each at the interface with 1yz4SO4101 (sulfate ion). The following table type in the bracket; noc/bb: number of contacts with the ligand, with the num- (Table 5) suggests possible disruptive replacements for these residues ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) (see Section 3.6). Table 4. res type subst’s cvg noc/ dist Table 5. (%) bb (A˚ ) res type disruptive 57 D D(100) 0.03 12/0 3.79 mutations 91 G G(100) 0.03 11/11 2.79 57 D (R)(FWH)(KYVCAG)(TQM) 93 S S(100) 0.03 17/12 3.01 91 G (KER)(FQMWHD)(NYLPI)(SVA) 94 R R(100) 0.03 30/8 2.66 93 S (KR)(FQMWH)(NYELPI)(D) continued in next column continued in next column 3 Table 5. continued Table 6. continued res type disruptive res type subst’s cvg noc/ dist mutations (%) bb (A˚ ) 94 R (TD)(SYEVCLAPIG)(FMW)(N) T(5) 95 S (KR)(QH)(FYEMW)(N) L(3) 88 S (KR)(FMWH)(Q)(E) V(1) 90 A (KER)(Y)(D)(Q) Q(1) .(5) Table 5. List of disruptive mutations for the top 25% of residues in H(1) 1yz4A, that are at the interface with sulfate ion. Table 6. The top 25% of residues in 1yz4A at the interface with 1yz4B. (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. ) Table 7. res type disruptive mutations 73 F (E)(T)(K)(D) 50 Y (K)(Q)(M)(ER) Table 7. List of disruptive mutations for the top 25% of residues in 1yz4A, that are at the interface with 1yz4B. Fig. 5. Residues in 1yz4A, at the interface with sulfate ion, colored by their 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 of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1yz4A.) Figure 5 shows residues in 1yz4A colored by their importance, at the interface with 1yz4SO4101. Interface with 1yz4B.Table 6 lists the top 25% of residues at the interface with 1yz4B. The following table (Table 7) suggests possible disruptive replacements for these residues (see Section 3.6).
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