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1Ki9 Lichtarge Lab 2006 Pages 1–7 1ki9 Evolutionary trace report by report maker July 15, 2010 4.3.1 Alistat 6 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ki9): Title: Adenylate kinase from methanococcus thermolithotrophicus Compound: Mol id: 1; molecule: adenylate kinase; chain: a, b, c; synonym: atp-amp transphosphorylase; ec: 2.7.4.3; engineered: yes Organism, scientific name: Methanococcus Thermolithotrophicus; 1ki9 contains a single unique chain 1ki9A (191 residues long) and its homologues 1ki9C and 1ki9B. CONTENTS 2 CHAIN 1KI9A 2.1 P43410 overview 1 Introduction 1 From SwissProt, id P43410, 92% identical to 1ki9A: 2 Chain 1ki9A 1 Description: Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphos- 2.1 P43410 overview 1 phorylase). 2.2 Multiple sequence alignment for 1ki9A 1 Organism, scientific name: Methanococcus thermolithotrophicus. 2.3 Residue ranking in 1ki9A 1 Taxonomy: Archaea; Euryarchaeota; Methanococci; Methanococca- 2.4 Top ranking residues in 1ki9A and their position on les; Methanococcaceae; Methanothermococcus. the structure 2 Catalytic activity: ATP + AMP = 2 ADP. 2.4.1 Clustering of residues at 25% coverage. 2 Biophysicochemical properties: 2.4.2 Overlap with known functional surfaces at Temperature dependence: Active from 60 to 80 degrees Celsius; 25% coverage. 2 Subunit: Monomer (Probable). 2.4.3 Possible novel functional surfaces at 25% Subcellular location: Cytoplasmic. coverage. 3 Similarity: Belongs to the archaeal adenylate kinase family. About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 5 collaboration between the Swiss Institute of Bioinformatics and the 3.1 Coverage 5 EMBL outstation - the European Bioinformatics Institute. There are 3.2 Known substitutions 5 no restrictions on its use as long as its content is in no way modified 3.3 Surface 5 and this statement is not removed. 3.4 Number of contacts 5 3.5 Annotation 5 2.2 Multiple sequence alignment for 1ki9A 3.6 Mutation suggestions 5 For the chain 1ki9A, the alignment 1ki9A.msf (attached) with 48 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 5 database, and fragments shorter than 75% of the query as well as 4.1 File formats 5 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 6 to this report, under the name of 1ki9A.msf. Its statistics, from the 4.3 Credits 6 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 2-192 in 1ki9A colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Format: MSF Number of sequences: 48 Total number of residues: 8818 Smallest: 147 Largest: 191 Average length: 183.7 Alignment length: 191 Average identity: 43% Most related pair: 98% Fig. 2. Residues in 1ki9A, colored by their relative importance. Clockwise: Most unrelated pair: 25% front, back, top and bottom views. Most distant seq: 36% Furthermore, 2% of residues show as conserved in this alignment. The alignment consists of 4% prokaryotic, and 37% archaean sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1ki9A.descr. 2.3 Residue ranking in 1ki9A The 1ki9A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1ki9A can be found in the file called 1ki9A.ranks sorted in the attachment. 2.4 Top ranking residues in 1ki9A and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 1ki9A colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they Fig. 3. Residues in 1ki9A, colored according to the cluster they belong to: belong to. The clusters in Fig.3 are composed of the residues listed red, followed by blue and yellow are the largest clusters (see Appendix for in Table 1. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 1. cluster size member Table 1. continued color residues cluster size member red 44 10,12,13,15,18,38,40,43,47 color residues 56,57,60,62,67,70,71,74,75 103,104,105,106,109,122,128 78,90,91,92,93,95,97,100,102 131,132,135,138,140,141,155 continued in next column 156,162,175 continued in next column 2 Table 1. continued cluster size member color residues Table 1. Clusters of top ranking residues in 1ki9A. 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 1ki9C.Table 2 lists the top 25% of residues at the interface with 1ki9C. 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˚ ) 122 E E(87) 0.16 1/0 4.65 T(8) Y(2) S(2) 167 G E(12) 0.17 17/17 3.66 G(70) Fig. 4. Residues in 1ki9A, at the interface with 1ki9C, colored by their rela- N(10) tive importance. 1ki9C is shown in backbone representation (See Appendix A(4) for the coloring scheme for the protein chain 1ki9A.) .(2) 156 R R(85) 0.19 30/6 3.34 D(8) Q(4) S(2) 170 V V(72) 0.23 50/41 2.60 I(14) M(10) .(2) Table 2. The top 25% of residues in 1ki9A at the interface with 1ki9C. (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 3. res type disruptive mutations 122 E (FWHR)(KVA)(YCG)(NLPI) 167 G (R)(H)(K)(FW) 156 R (TY)(FVCAWDG)(LPI)(SE) 170 V (Y)(R)(KEH)(D) Table 3. List of disruptive mutations for the top 25% of residues in 1ki9A, that are at the interface with 1ki9C. Figure 4 shows residues in 1ki9A colored by their importance, at the interface with 1ki9C. Interface with 1ki9B.Table 4 lists the top 25% of residues at the interface with 1ki9B. The following table (Table 5) suggests possible disruptive replacements for these residues (see Section 3.6). 3 Table 4. res type subst’s cvg noc/ dist (%) bb (A˚ ) 100 G G(100) 0.03 25/25 3.71 106 P P(100) 0.03 11/8 3.65 105 L L(95) 0.12 4/4 3.86 I(2) F(2) 103 P P(77) 0.17 38/3 3.35 A(12) L(8) I(2) 97 T I(10) 0.19 1/1 4.75 T(81) S(6) M(2) 102 L Y(25) 0.21 16/7 3.39 L(64) W(8) M(2) 162 Y A(12) 0.21 9/0 3.55 Y(54) C(14) Fig. 5. Residues in 1ki9A, at the interface with 1ki9B, colored by their rela- L(2) tive importance. 1ki9B is shown in backbone representation (See Appendix S(14) for the coloring scheme for the protein chain 1ki9A.) .(2) Table 4. The top 25% of residues in 1ki9A at the interface with 1ki9B. (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 5. res type disruptive mutations Fig. 6. A possible active surface on the chain 1ki9A. The larger cluster it 100 G (KER)(FQMWHD)(NYLPI)(SVA) belongs to is shown in blue. 106 P (YR)(TH)(SKECG)(FQWD) 105 L (R)(Y)(T)(KE) 103 P (YR)(H)(T)(KE) 6, while Table 7 suggests possible disruptive replacements for these 97 T (R)(K)(H)(FW) residues (see Section 3.6). 102 L (R)(TY)(K)(EH) Table 6. 162 Y (K)(Q)(R)(M) res type substitutions(%) cvg 43 M M(100) 0.03 Table 5. List of disruptive mutations for the top 25% of residues in 1ki9A, 92 H H(100) 0.03 that are at the interface with 1ki9B. 100 G G(100) 0.03 106 P P(100) 0.03 131 R R(100) 0.03 Figure 5 shows residues in 1ki9A colored by their importance, at the 90 D D(97)T(2) 0.04 interface with 1ki9B. 135 D D(97)K(2) 0.04 2.4.3 Possible novel functional surfaces at 25% coverage. One 140 R R(97)Y(2) 0.04 group of residues is conserved on the 1ki9A surface, away from (or 56 R R(97)L(2) 0.07 susbtantially larger than) other functional sites and interfaces reco- 71 Q Q(97)W(2) 0.07 gnizable in PDB entry 1ki9.
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