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1S04 Lichtarge Lab 2006 Pages 1–6 1s04 Evolutionary trace report by report maker June 12, 2010 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1s04): Title: Solution nmr structure of protein pf0455 from pyrococcus furiosus. northeast structural genomics consortium target pfr13 Compound: Mol id: 1; molecule: hypothetical protein pf0455; chain: a; engineered: yes CONTENTS Organism, scientific name: Pyrococcus Furiosus; 1s04 contains a single unique chain 1s04A (110 residues long). 1 Introduction 1 This is an NMR-determined structure – in this report the first model 2 Chain 1s04A 1 in the file was used. 2.1 Q8U3L1 overview 1 2.2 Multiple sequence alignment for 1s04A 1 2.3 Residue ranking in 1s04A 1 2.4 Top ranking residues in 1s04A and their position on the structure 1 2.4.1 Clustering of residues at 25% coverage. 1 2 CHAIN 1S04A 2.4.2 Possible novel functional surfaces at 25% 2.1 Q8U3L1 overview coverage. 2 From SwissProt, id Q8U3L1, 83% identical to 1s04A: Description: Hypothetical protein PF0455. 3 Notes on using trace results 4 Organism, scientific name: Pyrococcus furiosus. 3.1 Coverage 4 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 3.2 Known substitutions 4 les; Thermococcaceae; Pyrococcus. 3.3 Surface 4 3.4 Number of contacts 4 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 1s04A 4 Appendix 4 For the chain 1s04A, the alignment 1s04A.msf (attached) with 30 4.1 File formats 4 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 5 database, and fragments shorter than 75% of the query as well as 4.3 Credits 5 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 5 to this report, under the name of 1s04A.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-110 in 1s04A colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Format: MSF Number of sequences: 30 Total number of residues: 3144 Smallest: 86 Largest: 110 Average length: 104.8 Alignment length: 110 Average identity: 35% Most related pair: 98% Most unrelated pair: 17% Most distant seq: 39% Fig. 2. Residues in 1s04A, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 13% eukaryotic ( 13% plantae), 20% prokaryotic, and 30% 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 1s04A.descr. 2.3 Residue ranking in 1s04A The 1s04A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1s04A can be found in the file called 1s04A.ranks sorted in the attachment. 2.4 Top ranking residues in 1s04A 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 1s04A 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. 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 1s04A, 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 Table 1. corresponding Pymol script is attached. cluster size member color residues red 24 5,7,15,18,20,23,24,25,34,37 Table 1. continued 38,40,42,51,57,60,64,67,90 cluster size member continued in next column color residues 95,99,100,102,103 blue 2 73,74 2 Table 1. Clusters of top ranking residues in 1s04A. Table 3. continued res type disruptive mutations 2.4.2 Possible novel functional surfaces at 25% coverage. One 7 L (YR)(H)(T)(KE) group of residues is conserved on the 1s04A surface, away from (or 15 I (Y)(R)(H)(T) susbtantially larger than) other functional sites and interfaces reco- 38 D (R)(K)(FWH)(Y) gnizable in PDB entry 1s04. It is shown in Fig. 4. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. Table 3. Disruptive mutations for the surface patch in 1s04A. Another group of surface residues is shown in Fig.5. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. Fig. 4. A possible active surface on the chain 1s04A. The larger cluster it belongs to is shown in blue. The residues belonging to this surface ”patch” are listed in Table Fig. 5. Another possible active surface on the chain 1s04A. The larger cluster 2, while Table 3 suggests possible disruptive replacements for these it belongs to is shown in blue. residues (see Section 3.6). Table 2. The residues belonging to this surface ”patch” are listed in Table res type substitutions(%) cvg 4, while Table 5 suggests possible disruptive replacements for these 42 F F(96)Q(3) 0.03 residues (see Section 3.6). 51 V V(96)L(3) 0.06 Table 4. 40 I I(86)L(13) 0.10 res type substitutions(%) cvg 37 G G(90)D(6).(3) 0.13 23 E E(96)R(3) 0.03 34 I I(76)V(3)L(16) 0.16 64 L I(3)L(56)Y(40) 0.04 M(3) 90 Y Y(90)H(6)A(3) 0.06 5 M .(10)M(53)L(36) 0.18 25 R R(93)K(3)G(3) 0.07 7 L L(66)V(20).(6) 0.22 99 G N(3)G(93).(3) 0.08 I(6) 57 Y Y(83)F(16) 0.09 15 I V(20)I(56)L(16) 0.24 60 F F(93)A(3)P(3) 0.12 M(6) 67 E E(59)I(26)L(6) 0.14 38 D D(80)S(6)A(6) 0.24 F(3)Y(3) .(3)H(3) 73 L L(36)F(16)D(26) 0.17 G(13)S(6) Table 2. Residues forming surface ”patch” in 1s04A. 74 P P(53)C(26)Y(6) 0.19 T(3)S(6)K(3) 95 E N(3)E(83)L(3) 0.21 Table 3. M(3)I(6) res type disruptive mutations Table 4. 42 F (TE)(KD)(SCG)(QR) Residues forming surface ”patch” in 1s04A. 51 V (YR)(KE)(H)(QD) 40 I (YR)(TH)(SKECG)(FQWD) Table 5. 37 G (R)(K)(FWH)(M) res type disruptive 34 I (Y)(R)(H)(T) mutations 5 M (Y)(T)(H)(CG) 23 E (FW)(YVCAHG)(T)(SLPIR) continued in next column continued in next column 3 Table 5. continued 3.4 Number of contacts res type disruptive Another column worth noting is denoted “noc/bb”; it tells the num- mutations ber of contacts heavy atoms of the residue in question make across 64 L (R)(Y)(T)(KH) the interface, as well as how many of them are realized through the 90 Y (K)(Q)(EM)(R) backbone atoms (if all or most contacts are through the backbone, 25 R (D)(TY)(E)(SFVLAWPI) mutation presumably won’t have strong impact). Two heavy atoms 99 G (R)(E)(K)(FWH) are considered to be “in contact” if their centers are closer than 5A˚ . 57 Y (K)(Q)(EM)(NR) 60 F (KE)(TQDR)(SNCG)(Y) 3.5 Annotation 67 E (R)(H)(CG)(FW) 73 L (R)(Y)(KH)(TE) If the residue annotation is available (either from the pdb file or 74 P (R)(Y)(H)(K) from other sources), another column, with the header “annotation” 95 E (H)(Y)(FWR)(CG) appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide bond forming residue), hb (hydrogen bond forming residue, jb (james Table 5. Disruptive mutations for the surface patch in 1s04A. bond forming residue), and sb (for salt bridge forming residue). 3.6 Mutation suggestions 3 NOTES ON USING TRACE RESULTS Mutation suggestions are completely heuristic and based on comple- 3.1 Coverage mentarity with the substitutions found in the alignment. Note that Trace results are commonly expressed in terms of coverage: the resi- they are meant to be disruptive to the interaction of the protein due is important if its “coverage” is small - that is if it belongs to with its ligand. The attempt is made to complement the following some small top percentage of residues [100% is all of the residues properties: small [AV GSTC], medium [LPNQDEMIK], large in a chain], according to trace. The ET results are presented in the [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- form of a table, usually limited to top 25% percent of residues (or tively [KHR], or negatively [DE] charged, aromatic [WFYH], to some nearby percentage), sorted by the strength of the presumed long aliphatic chain [EKRQM], OH-group possession [SDETY ], evolutionary pressure.
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