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1Wde Lichtarge Lab 2006 Pages 1–6 1wde Evolutionary trace report by report maker March 16, 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 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1wde): Title: Crystal structure of the conserved hypothetical protein ape0931 from aeropyrum pernix k1 Compound: Mol id: 1; molecule: probable diphthine synthase; chain: a; synonym: diphthamide biosynthesis methyltransferase, conserved hypothetical protein ape0931; ec: 2.1.1.98; engineered: yes Organism, scientific name: Aeropyrum Pernix; 1wde contains a single unique chain 1wdeA (289 residues long). CONTENTS 2 CHAIN 1WDEA 1 Introduction 1 2.1 Q9YDI2 overview 2 Chain 1wdeA 1 From SwissProt, id Q9YDI2, 87% identical to 1wdeA: 2.1 Q9YDI2 overview 1 Description: Probable diphthine synthase (EC 2.1.1.98) (Diphtha- 2.2 Multiple sequence alignment for 1wdeA 1 mide biosynthesis methyltransferase). 2.3 Residue ranking in 1wdeA 1 Organism, scientific name: Aeropyrum pernix. 2.4 Top ranking residues in 1wdeA and their position on Taxonomy: Archaea; Crenarchaeota; Thermoprotei; Desulfurococ- the structure 2 cales; Desulfurococcaceae; Aeropyrum. 2.4.1 Clustering of residues at 25% coverage. 2 Function: Required for the methylation step in diphthamide biosyn- 2.4.2 Possible novel functional surfaces at 25% thesis (By similarity). coverage. 2 Catalytic activity: S-adenosyl-L-methionine + 2-(3-carboxy-3- aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3- 3 Notes on using trace results 4 carboxy-3-(methylammonio)propyl)-L-histidine. 3.1 Coverage 4 Pathway: Diphthamide biosynthesis; second step. 3.2 Known substitutions 4 Similarity: Belongs to the diphthine synthase family. 3.3 Surface 4 About: This Swiss-Prot entry is copyright. It is produced through a 3.4 Number of contacts 4 collaboration between the Swiss Institute of Bioinformatics and the 3.5 Annotation 4 EMBL outstation - the European Bioinformatics Institute. There are 3.6 Mutation suggestions 5 no restrictions on its use as long as its content is in no way modified and this statement is not removed. 4 Appendix 5 4.1 File formats 5 2.2 Multiple sequence alignment for 1wdeA 4.2 Color schemes used 5 For the chain 1wdeA, the alignment 1wdeA.msf (attached) with 43 4.3 Credits 5 sequences was used. The alignment was downloaded from the HSSP 4.3.1 Alistat 5 database, and fragments shorter than 75% of the query as well as 4.3.2 CE 5 duplicate sequences were removed. It can be found in the attachment 1 Lichtarge lab 2006 Fig. 1. Residues 6-149 in 1wdeA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Fig. 2. Residues 150-294 in 1wdeA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Fig. 3. Residues in 1wdeA, colored by their relative importance. Clockwise: front, back, top and bottom views. to this report, under the name of 1wdeA.msf. Its statistics, from the alistat program are the following: 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Format: MSF top 25% of all residues, this time colored according to clusters they Number of sequences: 43 belong to. The clusters in Fig.4 are composed of the residues listed Total number of residues: 10916 Smallest: 231 Largest: 289 Average length: 253.9 Alignment length: 289 Average identity: 37% Most related pair: 99% Most unrelated pair: 18% Most distant seq: 36% Furthermore, 4% of residues show as conserved in this alignment. The alignment consists of 2% eukaryotic, 4% prokaryotic, and 23% 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 1wdeA.descr. 2.3 Residue ranking in 1wdeA The 1wdeA sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues in 1wdeA can be found in the file called 1wdeA.ranks sorted in the attachment. 2.4 Top ranking residues in 1wdeA and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1wdeA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for residues in the protein . Figure 3 shows residues in 1wdeA colored the coloring scheme). Clockwise: front, back, top and bottom views. The by their importance: bright red and yellow indicate more conser- corresponding Pymol script is attached. ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. in Table 1. 2 Table 1. cluster size member color residues red 66 10,14,15,16,17,23,26,27,36 37,39,41,42,65,67,70,71,88 89,90,91,92,93,94,97,98,99 100,102,103,107,111,117,118 119,120,121,125,126,128,131 132,133,135,136,137,138,142 143,145,146,162,166,167,168 169,172,173,174,175,219,241 243,244,245,257 Table 1. Clusters of top ranking residues in 1wdeA. 2.4.2 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1wdeA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1wde. It is shown in Fig. 5. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. Fig. 5. A possible active surface on the chain 1wdeA. The larger cluster it belongs to is shown in blue. The residues belonging to this surface ”patch” are listed in Table 2, while Table 3 suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type substitutions(%) cvg 41 Y Y(100) 0.04 42 T T(100) 0.04 67 R R(100) 0.04 71 E E(100) 0.04 93 D D(100) 0.04 98 T T(100) 0.04 100 H H(100) 0.04 135 Y Y(100) 0.04 138 G G(100) 0.04 132 L L(97)M(2) 0.05 121 S S(93)T(6) 0.06 162 N N(97).(2) 0.06 continued in next column 3 Table 2. continued Table 2. continued res type substitutions(%) cvg res type substitutions(%) cvg 137 F F(83)Y(2)L(13) 0.07 219 G R(76)G(9).(6) 0.21 174 D D(93)E(4)K(2) 0.07 K(4)V(2) 70 L V(65)L(30)I(4) 0.08 118 P P(44)N(11)H(41) 0.22 97 A A(81)S(18) 0.08 S(2) 173 L V(4)L(93)R(2) 0.09 241 E E(20)G(69)P(4) 0.22 10 L L(93)F(6) 0.10 Q(2)L(2) 17 Y L(81)Y(4)P(11) 0.10 27 L L(67)A(6)K(2) 0.23 I(2) I(13)M(2)R(6) 23 T T(76)N(2)S(20) 0.11 91 A V(34)P(11)A(34) 0.23 142 T S(51)T(48) 0.11 G(16)I(2) 99 T T(86)A(9)S(4) 0.12 120 V A(48)V(27)P(11) 0.23 133 S Q(72)E(2)S(20) 0.12 L(2)S(6)I(2) H(4) 143 L M(25)I(34)L(18) 0.23 131 X G(83)M(2)C(11) 0.13 V(20) X(2) 103 L L(86)V(2)I(9) 0.24 221 G G(90).(4)P(2) 0.13 M(2) W(2) 40 S A(32)T(11)S(9) 0.25 65 A A(48)C(2)L(39) 0.14 I(2)F(27)D(11) R(6)V(2) Y(2)E(2) 102 S D(62)A(25)S(6) 0.14 E(4) Table 2. Residues forming surface ”patch” in 1wdeA. 175 V I(74)V(16)T(2) 0.14 L(6) 166 G G(83)N(11)D(2) 0.15 Table 3. .(2) res type disruptive 172 L L(69)F(18)G(2) 0.15 mutations Y(9) 41 Y (K)(QM)(NEVLAPIR)(D) 128 G G(69)S(23)A(4) 0.16 42 T (KR)(FQMWH)(NELPI)(D) D(2) 67 R (TD)(SYEVCLAPIG)(FMW)(N) 117 I V(23)I(74)R(2) 0.17 71 E (FWH)(YVCARG)(T)(SNKLPI) 136 R N(25)R(46)K(27) 0.17 93 D (R)(FWH)(KYVCAG)(TQM) 245 Y H(76)Q(2)Y(4) 0.17 98 T (KR)(FQMWH)(NELPI)(D) V(9)A(2)G(2) 100 H (E)(TQMD)(SNKVCLAPIG)(YR) S(2) 135 Y (K)(QM)(NEVLAPIR)(D) 119 G N(39)G(44)A(13) 0.18 138 G (KER)(FQMWHD)(NYLPI)(SVA) S(2) 132 L (Y)(R)(TH)(SCG) 125 A S(41)A(51)N(4) 0.18 121 S (KR)(FQMWH)(NELPI)(Y) L(2) 162 N (Y)(FTWH)(SVCAG)(ER) 257 E L(18)A(2)E(67) 0.18 137 F (K)(E)(Q)(R) .(9)M(2) 174 D (FW)(HR)(Y)(VCAG) 244 V L(65)P(18)V(6) 0.19 70 L (YR)(H)(T)(KE) A(9) 97 A (KR)(YE)(QH)(D) 19 P D(69)P(16)A(4) 0.20 173 L (Y)(T)(R)(H) C(2)N(2)I(2) 10 L (R)(TY)(KE)(SCHG) R(2) 17 Y (K)(R)(Q)(E) 167 L L(86)M(2)Y(2) 0.20 23 T (R)(K)(FWH)(M) A(2)F(2).(2) 142 T (KR)(FQMWH)(NELPI)(D) S(2) 99 T (KR)(QH)(FMW)(E) 243 G G(11)P(83)Q(2) 0.20 133 S (R)(FKW)(H)(YM) I(2) 131 X (R)(KYE)(H)(FWD) 37 Y Y(62)L(4)F(27) 0.21 221 G (KER)(QD)(H)(M) W(2)A(2) 65 A (E)(Y)(KR)(D) continued in next column continued in next column 4 Table 3.
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