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1Vbf Lichtarge Lab 2006 Pages 1–8 1vbf Evolutionary trace report by report maker July 2, 2010 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 8 4.6 About report maker 8 4.7 Attachments 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1vbf): Title: Crystal structure of protein l-isoaspartate o- methyltransferase homologue from sulfolobus tokodaii CONTENTS Compound: Mol id: 1; molecule: 231aa long hypothetical protein-l- isoaspartate o- methyltransferase; chain: a, b, c, d; synonym: protein 1 Introduction 1 l-isoaspartate o-methyltransferase; ec: 2.1.1.77; engineered: yes Organism, scientific name: Sulfolobus Tokodaii; 2 Chain 1vbfB 1 1vbf contains a single unique chain 1vbfB (226 residues long) and 2.1 Q972K9 overview 1 its homologues 1vbfA, 1vbfD, and 1vbfC. 2.2 Multiple sequence alignment for 1vbfB 1 2.3 Residue ranking in 1vbfB 1 2.4 Top ranking residues in 1vbfB and their position on the structure 2 2.4.1 Clustering of residues at 25% coverage. 2 2 CHAIN 1VBFB 2.4.2 Overlap with known functional surfaces at 2.1 Q972K9 overview 25% coverage. 2 2.4.3 Possible novel functional surfaces at 25% From SwissProt, id Q972K9, 92% identical to 1vbfB: coverage. 5 Description: Hypothetical protein ST1123. Organism, scientific name: Sulfolobus tokodaii. 3 Notes on using trace results 6 Taxonomy: Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; 3.1 Coverage 6 Sulfolobaceae; Sulfolobus. 3.2 Known substitutions 6 3.3 Surface 6 3.4 Number of contacts 6 3.5 Annotation 6 2.2 Multiple sequence alignment for 1vbfB 3.6 Mutation suggestions 6 For the chain 1vbfB, the alignment 1vbfB.msf (attached) with 327 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 7 database, and fragments shorter than 75% of the query as well as 4.1 File formats 7 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 7 to this report, under the name of 1vbfB.msf. Its statistics, from the 4.3 Credits 7 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-113 in 1vbfB colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 2. Residues 114-226 in 1vbfB colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 3. Residues in 1vbfB, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 327 Total number of residues: 61703 Smallest: 76 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 226 Average length: 188.7 Alignment length: 226 Average identity: 41% Most related pair: 99% Most unrelated pair: 10% Most distant seq: 30% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of <1% eukaryotic ( <1% vertebrata), 14% prokaryotic, and 6% archaean sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1vbfB.descr. 2.3 Residue ranking in 1vbfB The 1vbfB sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1vbfB can be found in the file called 1vbfB.ranks sorted in the attachment. 2.4 Top ranking residues in 1vbfB and their position on the structure Fig. 4. Residues in 1vbfB, colored according to the cluster they belong to: In the following we consider residues ranking among top 25% of resi- red, followed by blue and yellow are the largest clusters (see Appendix for dues in the protein . Figure 3 shows residues in 1vbfB colored by their the coloring scheme). Clockwise: front, back, top and bottom views. The importance: bright red and yellow indicate more conserved/important corresponding Pymol script is attached. residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. in Table 1. 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the top 25% of all residues, this time colored according to clusters they 2 Table 1. Table 3. cluster size member res type disruptive color residues mutations red 55 24,25,28,37,38,45,46,47,51 46 P (R)(Y)(H)(T) 52,53,54,55,56,62,66,74,75 47 I (R)(Y)(K)(E) 76,78,79,80,81,82,83,84,85 40 H (E)(T)(Q)(D) 86,88,95,99,100,104,108,112 45 L (R)(Y)(H)(K) 124,125,128,134,135,136,138 141,142,148,151,154,155,159 Table 3. List of disruptive mutations for the top 25% of residues in 1vbfB, 164,166,171,191,193,194 that are at the interface with 1vbfD2. Table 1. Clusters of top ranking residues in 1vbfB. 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 1vbfD2.By analogy with 1vbfC – 1vbfD2 inter- face. Table 2 lists the top 25% of residues at the interface with 1vbfD2. 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˚ ) 46 P G(7) 0.17 38/7 2.98 P(79)DQ TNE(2)Y .(1) S(3) A(1)RV 47 I Y(4) 0.20 28/22 2.39 I(86)F L(3)G .(1)HMC S Fig. 5. Residues in 1vbfB, at the interface with 1vbfD2, colored by their rela- 40 H D(68) 0.22 4/0 4.20 tive importance. 1vbfD2 is shown in backbone representation (See Appendix N(22)G for the coloring scheme for the protein chain 1vbfB.) Y(1) H(2) L(1)SKP Figure 5 shows residues in 1vbfB colored by their importance, at the .(1)AI interface with 1vbfD2. 45 L I(8) 0.23 1/0 4.39 Interface with 1vbfA.Table 4 lists the top 25% of residues at the V(2) interface with 1vbfA. The following table (Table 5) suggests possible L(80) disruptive replacements for these residues (see Section 3.6). F(4) Table 4. .(2)PMT res type subst’s cvg noc/ dist AY (%) bb (A˚ ) 148 L P(92)DS 0.07 2/2 4.59 Table 2. The top 25% of residues in 1vbfB at the interface with 1vbfD2. IV(1) (Field names: res: residue number in the PDB entry; type: amino acid type; L(2).AH substs: substitutions seen in the alignment; with the percentage of each type M in the bracket; noc/bb: number of contacts with the ligand, with the number of 166 G G(88)S 0.16 8/8 3.10 contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) E(1) A(2)LWI KMQP continued in next column 3 Table 4. continued Table 6. res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) .(1)TDV 95 V TV(88) 0.12 9/9 3.71 R L(6)AN I(4) Table 4. The top 25% of residues in 1vbfB at the interface with 1vbfA. (Field names: res: residue number in the PDB entry; type: amino acid type; Table 6. The top 25% of residues in 1vbfB at the interface with 1vbfC. substs: substitutions seen in the alignment; with the percentage of each type (Field names: res: residue number in the PDB entry; type: amino acid type; in the bracket; noc/bb: number of contacts with the ligand, with the number of substs: substitutions seen in the alignment; with the percentage of each type contacts realized through backbone atoms given in the bracket; dist: distance in the bracket; noc/bb: number of contacts with the ligand, with the number of of closest apporach to the ligand. ) contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 5. res type disruptive Table 7. mutations res type disruptive 148 L (R)(Y)(H)(T) mutations 166 G (R)(K)(E)(H) 95 V (R)(Y)(KE)(H) Table 5. List of disruptive mutations for the top 25% of residues in 1vbfB, Table 7. List of disruptive mutations for the top 25% of residues in 1vbfB, that are at the interface with 1vbfA. that are at the interface with 1vbfC. Fig. 6. Residues in 1vbfB, at the interface with 1vbfA, colored by their rela- Fig. 7. Residues in 1vbfB, at the interface with 1vbfC, colored by their rela- tive importance. 1vbfA is shown in backbone representation (See Appendix tive importance. 1vbfC is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 1vbfB.) for the coloring scheme for the protein chain 1vbfB.) Figure 6 shows residues in 1vbfB colored by their importance, at the Figure 7 shows residues in 1vbfB colored by their importance, at the interface with 1vbfA. interface with 1vbfC. Interface with 1vbfC.Table 6 lists the top 25% of residues at the interface with 1vbfC. The following table (Table 7) suggests possible 2.4.3 Possible novel functional surfaces at 25% coverage. One disruptive replacements for these residues (see Section 3.6).
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