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Pages 1–7 1e5o Evolutionary trace report by report maker September 20, 2008 4.3.1 Alistat 6 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 7 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1e5o): Title: Endothiapepsin complex with inhibitor db2 Compound: Mol id: 1; molecule: endothiapepsin; chain: e; frag- ment: residue 90-419; ec: 3.4.23.23; mol id: 2; molecule: endothia- pepsin inhibitor; chain: i Organism, scientific name: Endothia Parasitica; 1e5o contains a single unique chain 1e5oE (330 residues long). Chain 1e5oI is too short (4 residues) to permit statistically significant CONTENTS analysis, and was treated as a peptide ligand. 1 Introduction 1 2 CHAIN 1E5OE 2.1 P11838 overview 2 Chain 1e5oE 1 2.1 P11838 overview 1 From SwissProt, id P11838, 90% identical to 1e5oE: 2.2 Multiple sequence alignment for 1e5oE 1 Description: Endothiapepsin precursor (EC 3.4.23.22) (Aspartate 2.3 Residue ranking in 1e5oE 1 protease). 2.4 Top ranking residues in 1e5oE and their position on Organism, scientific name: Cryphonectria parasitica (Chesnut the structure 2 blight fungus) (Endothia parasitica). 2.4.1 Clustering of residues at 25% coverage. 2 Taxonomy: Eukaryota; Fungi; Ascomycota; Pezizomycotina; 2.4.2 Overlap with known functional surfaces at Sordariomycetes; Sordariomycetidae; Diaporthales; Valsaceae; 25% coverage. 3 Cryphonectria-Endothia complex; Cryphonectria. 2.4.3 Possible novel functional surfaces at 25% Catalytic activity: Hydrolysis of proteins with specificity similar to coverage. 3 that of pepsin A, prefers hydrophobic residues at P1 and P1', but does not cleave 14-Ala-—-Leu-15 in the B chain of insulin or Z-Glu-Tyr. 3 Notes on using trace results 5 Clots milk. 3.1 Coverage 5 Similarity: Belongs to the peptidase A1 family. 3.2 Known substitutions 5 About: This Swiss-Prot entry is copyright. It is produced through a 3.3 Surface 6 collaboration between the Swiss Institute of Bioinformatics and the 3.4 Number of contacts 6 EMBL outstation - the European Bioinformatics Institute. There are 3.5 Annotation 6 no restrictions on its use as long as its content is in no way modified 3.6 Mutation suggestions 6 and this statement is not removed. 4 Appendix 6 2.2 Multiple sequence alignment for 1e5oE 4.1 File formats 6 For the chain 1e5oE, the alignment 1e5oE.msf (attached) with 114 4.2 Color schemes used 6 sequences was used. The alignment was assembled through combi- 4.3 Credits 6 nation of BLAST searching on the UniProt database and alignment 1 Lichtarge lab 2006 2.4 Top ranking residues in 1e5oE and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 3 shows residues in 1e5oE 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. Fig. 1. Residues -2-159 in 1e5oE colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Note that some residues in 1e5oE carry insertion code. Fig. 2. Residues 162-326 in 1e5oE colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Note that some residues in 1e5oE carry insertion code. using Muscle program. It can be found in the attachment to this Fig. 3. Residues in 1e5oE, colored by their relative importance. Clockwise: alistat report, under the name of 1e5oE.msf. Its statistics, from the front, back, top and bottom views. program are the following: Format: MSF Number of sequences: 114 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 35559 top 25% of all residues, this time colored according to clusters they Smallest: 270 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 330 in Table 1. Average length: 311.9 Alignment length: 330 Table 1. Average identity: 36% cluster size member Most related pair: 98% color residues Most unrelated pair: 17% red 82 11,14,18,21,23,25,29,31,32 Most distant seq: 32% 33,34,35,36,37,38,39,40,42 45,56,61,63,71,73,75,76,77 78,80,82,87,99,101,102,104 Furthermore, 1% of residues show as conserved in this alignment. 108,111,118,119,120,121,122 The alignment consists of 99% eukaryotic ( 34% vertebrata, 5% 123,137,146,151,153,155,167 arthropoda, 43% fungi) sequences. (Descriptions of some sequences 168,171,175,177,190,213,214 were not readily available.) The file containing the sequence descrip- 215,216,217,218,219,220,224 tions can be found in the attachment, under the name 1e5oE.descr. 250,255,273,283,285,286,300 301,303,304,306,307,308,311 2.3 Residue ranking in 1e5oE 313,314,315,322,324 The 1e5oE sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues Table 1. Clusters of top ranking residues in 1e5oE. in 1e5oE can be found in the file called 1e5oE.ranks sorted in the attachment. 2 Table 2. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) V(7) L(9)TMK 76 G G(91) 0.13 19/19 2.79 E(2) V(1)D.I PA 213 I I(84) 0.13 4/0 4.04 L(3) V(6) A(3) T(2) 111 F F(71) 0.14 8/0 3.98 .(6) L(12) Y(1) M(3) E(1)VTQ A 77 D S(24) 0.21 11/0 2.97 Fig. 4. Residues in 1e5oE, colored according to the cluster they belong to: D(35) red, followed by blue and yellow are the largest clusters (see Appendix for T(36)K. the coloring scheme). Clockwise: front, back, top and bottom views. The LG corresponding Pymol script is attached. Table 2. The top 25% of residues in 1e5oE at the interface with 1e5oI. (Field names: res: residue number in the PDB entry; type: amino acid type; 2.4.2 Overlap with known functional surfaces at 25% coverage. substs: substitutions seen in the alignment; with the percentage of each type The name of the ligand is composed of the source PDB identifier in the bracket; noc/bb: number of contacts with the ligand, with the number of and the heteroatom name used in that file. contacts realized through backbone atoms given in the bracket; dist: distance Interface with the peptide 1e5oI. Table 2 lists the top 25% of of closest apporach to the ligand. ) residues at the interface with 1e5oI. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Table 3. res type subst’s cvg noc/ dist antn res type disruptive (%) bb (A˚ ) mutations 32 D D(100) 0.01 21/0 2.85 site 32 D (R)(FWH)(KYVCAG)(TQM) 215 D D(100) 0.01 19/0 2.95 site 215 D (R)(FWH)(KYVCAG)(TQM) 35 S S(98) 0.02 11/7 3.70 35 S (KR)(FQMWH)(E)(NYLPI) G(1) 217 G (KR)(E)(FQMWH)(D) 217 G G(99)S 0.02 20/20 3.19 34 G (KR)(E)(QH)(D) 34 G G(97)VA 0.04 25/25 3.04 75 Y (KM)(EVQLAPI)(ND)(SCRG) T 218 T (KR)(FQMWH)(NELPI)(D) 75 Y Y(98) 0.04 74/26 3.13 120 L (R)(Y)(H)(K) R(1) 301 I (R)(Y)(H)(K) 218 T T(97) 0.04 12/4 3.88 73 I (Y)(R)(H)(T) S(2) 76 G (R)(K)(H)(E) 120 L I(71) 0.06 9/0 3.70 213 I (R)(Y)(H)(K) L(27)T 111 F (K)(E)(R)(TQ) 301 I I(90) 0.10 4/0 3.70 77 D (R)(FWH)(Y)(K) V(3) L(5)T Table 3. List of disruptive mutations for the top 25% of residues in 73 I I(80) 0.12 3/0 4.35 1e5oE, that are at the interface with 1e5oI. continued in next column Figure 5 shows residues in 1e5oE colored by their importance, at the interface with 1e5oI. 3 Table 4. continued res type substitutions(%) cvg .(5)Q(1)S(2) 25 Q Q(83)T.(6)V(4) 0.18 K(1)RDEI 63 T T(86)S(11)KQ 0.22 Table 4. Residues forming surface ”patch” in 1e5oE. Table 5. res type disruptive mutations 21 G (KER)(FQMWHD)(NLPI)(Y) 61 S (R)(K)(H)(FW) 23 P (Y)(R)(H)(T) 25 Q (Y)(FWH)(T)(CG) 63 T (FW)(HR)(K)(M) Table 5. Disruptive mutations for the surface patch in 1e5oE. Another group of surface residues is shown in Fig.7. The right panel Fig. 5. Residues in 1e5oE, at the interface with 1e5oI, colored by their rela- tive importance. 1e5oI is shown in backbone representation (See Appendix shows (in blue) the rest of the larger cluster this surface belongs to. for the coloring scheme for the protein chain 1e5oE.) 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1e5oE surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1e5o.
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