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2Vtv Lichtarge Lab 2006

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2Vtv Lichtarge Lab 2006 Pages 1–7 2vtv Evolutionary trace report by report maker December 4, 2009 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 6 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2vtv): Title: Phaz7 depolymerase from paucimonas lemoignei CONTENTS Compound: Mol id: 1; molecule: phb depolymerase phaz7; chain: a, b; fragment: residues 39-380; ec: 3.1.1.75 1 Introduction 1 Organism, scientific name: Paucimonas Lemoignei 2vtv contains a single unique chain 2vtvA (340 residues long) and 2 Chain 2vtvA 1 its homologue 2vtvB. 2.1 Q939Q9 overview 1 2.2 Multiple sequence alignment for 2vtvA 1 2.3 Residue ranking in 2vtvA 1 2.4 Top ranking residues in 2vtvA and their position on the structure 2 2.4.1 Clustering of residues at 25% coverage. 2 2 CHAIN 2VTVA 2.4.2 Overlap with known functional surfaces at 2.1 Q939Q9 overview 25% coverage. 2 From SwissProt, id Q939Q9, 94% identical to 2vtvA: 2.4.3 Possible novel functional surfaces at 25% Description: PHB depolymerase PhaZ7 (Fragment). coverage. 3 Organism, scientific name: Pseudomonas lemoignei. Taxonomy: Bacteria; Proteobacteria; Betaproteobacteria; Burkhol- 3 Notes on using trace results 5 deriales; Burkholderiaceae; Paucimonas. 3.1 Coverage 5 3.2 Known substitutions 5 3.3 Surface 5 3.4 Number of contacts 5 3.5 Annotation 5 2.2 Multiple sequence alignment for 2vtvA 3.6 Mutation suggestions 5 For the chain 2vtvA, the alignment 2vtvA.msf (attached) with 11 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 2vtvA.msf. Its statistics, from the 4.3 Credits 6 alistat program are the following: 1 Lichtarge lab 2006 residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 1. Residues 1-170 in 2vtvA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 2. Residues 171-342 in 2vtvA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 3. Residues in 2vtvA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 11 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 2793 top 25% of all residues, this time colored according to clusters they Smallest: 179 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 340 in Table 1. Average length: 253.9 Table 1. Alignment length: 340 cluster size member Average identity: 37% color residues Most related pair: 97% red 83 29,30,38,40,42,43,44,45,46 Most unrelated pair: 23% 47,48,49,50,51,53,55,74,77 Most distant seq: 30% 81,82,85,86,87,88,89,91,92 93,94,104,105,106,107,114 117,118,119,121,122,123,124 Furthermore, 4% of residues show as conserved in this alignment. 125,126,129,130,132,133,135 The alignment consists of sequences. (Descriptions of some 136,137,138,139,140,141,142 sequences were not readily available.) The file containing the 143,145,146,155,156,158,159 sequence descriptions can be found in the attachment, under the name 160,161,162,163,164,165,166 2vtvA.descr. 167,168,170,171,174,175,182 2.3 Residue ranking in 2vtvA 183,184,185,196,197,199,201 The 2vtvA sequence is shown in Figs. 1–2, with each residue colored Table 1. Clusters of top ranking residues in 2vtvA. according to its estimated importance. The full listing of residues in 2vtvA can be found in the file called 2vtvA.ranks sorted in the attachment. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier 2.4 Top ranking residues in 2vtvA and their position on and the heteroatom name used in that file. the structure Glycerol binding site. Table 2 lists the top 25% of residues at the In the following we consider residues ranking among top 25% of resi- interface with 2vtvAGOL1343 (glycerol). The following table (Table dues in the protein . Figure 3 shows residues in 2vtvA colored by their 3) suggests possible disruptive replacements for these residues (see importance: bright red and yellow indicate more conserved/important Section 3.6). 2 Table 2. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 166 R L(45) 0.18 14/0 2.67 site Y(27) R(27) Table 2. The top 25% of residues in 2vtvA at the interface with glyce- rol.(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 num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 3. res type disruptive mutations 166 R (TD)(E)(VCAG)(S) Table 3. List of disruptive mutations for the top 25% of residues in 2vtvA, that are at the interface with glycerol. Fig. 4. Residues in 2vtvA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Fig. 5. Residues in 2vtvA, at the interface with glycerol, colored by their relative importance. The ligand (glycerol) 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 2vtvA.) Figure 5 shows residues in 2vtvA colored by their importance, at the interface with 2vtvAGOL1343. Interface with 2vtvB.Table 4 lists the top 25% of residues at the interface with 2vtvB. The following table (Table 5) suggests possible disruptive replacements for these residues (see Section 3.6). 3 Table 4. shows (in blue) the rest of the larger cluster this surface belongs to. res type subst’s cvg noc/ dist (%) bb (A˚ ) 201 G S(36) 0.24 4/4 4.16 .(9) Y(27) G(27) Table 4. The top 25% of residues in 2vtvA at the interface with 2vtvB. (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. 7. A possible active surface on the chain 2vtvA. The larger cluster it belongs to is shown in blue. Table 5. res type disruptive mutations The residues belonging to this surface ”patch” are listed in Table 201 G (K)(R)(E)(QM) 6, while Table 7 suggests possible disruptive replacements for these residues (see Section 3.6). Table 5. List of disruptive mutations for the top 25% of residues in 2vtvA, Table 6. that are at the interface with 2vtvB. res type substitutions(%) cvg antn 49 N N(100) 0.04 136 S S(100) 0.04 163 G G(100) 0.04 182 P P(90)S(9) 0.09 199 P P(90).(9) 0.09 146 L I(72)L(27) 0.12 168 L L(90)I(9) 0.12 50 G S(63)T(9)G(27) 0.13 142 S A(90)S(9) 0.13 164 G A(90)G(9) 0.13 104 N Q(36)N(63) 0.14 107 S S(81)D(18) 0.15 137 M M(81)L(18) 0.15 162 A A(90)G(9) 0.15 185 G G(63)S(36) 0.16 105 Y Y(63)N(9)S(27) 0.17 175 G G(63)P(9)T(27) 0.17 166 R L(45)Y(27)R(27) 0.18 site 197 F L(36).(9)F(54) 0.23 174 T A(36)Y(9)S(27) 0.24 T(27) 201 G S(36).(9)Y(27) 0.24 G(27) 102 Q Q(54)A(9)S(27) 0.25 Fig. 6. Residues in 2vtvA, at the interface with 2vtvB, colored by their rela- N(9) tive importance. 2vtvB is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 2vtvA.) Table 6. Residues forming surface ”patch” in 2vtvA. Figure 6 shows residues in 2vtvA colored by their importance, at the Table 7. interface with 2vtvB. res type disruptive mutations 2.4.3 Possible novel functional surfaces at 25% coverage. One 49 N (Y)(FTWH)(SEVCARG)(MD) group of residues is conserved on the 2vtvA surface, away from (or continued in next column susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 2vtv. It is shown in Fig. 7. The right panel 4 Table 7.
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