Pages 1–9 1j71 Evolutionary trace report by report maker September 24, 2010 4.3.1 Alistat 8 4.3.2 CE 8 4.3.3 DSSP 8 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 9 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1j71): Title: Structure of the extracellular aspartic proteinase from candida tropicalis yeast. Compound: Mol id: 1; molecule: aspartic proteinase; chain: a; synonym: candidapepsin; ec: 3.4.23.24; mol id: 2; molecule: tetra- peptide thr-ile-thr-ser; chain: b Organism, scientific name: Unidentified CONTENTS 1j71 contains a single unique chain 1j71A (334 residues long). 1 Introduction 1 Chain 1j71B is too short (4 residues) to permit statistically significant analysis, and was treated as a peptide ligand. 2 Chain 1j71A 1 2.1 Q00663 overview 1 2.2 Multiple sequence alignment for 1j71A 1 2 CHAIN 1J71A 2.3 Residue ranking in 1j71A 1 2.1 Q00663 overview 2.4 Top ranking residues in 1j71A and their position on the structure 1 From SwissProt, id Q00663, 98% identical to 1j71A: 2.4.1 Clustering of residues at 25% coverage. 2 Description: Candidapepsin precursor (EC 3.4.23.24) (Aspartate 2.4.2 Overlap with known functional surfaces at protease) (ACP). 25% coverage. 2 Organism, scientific name: Candida tropicalis (Yeast). 2.4.3 Possible novel functional surfaces at 25% Taxonomy: Eukaryota; Fungi; Ascomycota; Saccharomycotina; coverage. 5 Saccharomycetes; Saccharomycetales; mitosporic Saccharomyceta- les; Candida. 3 Notes on using trace results 7 Catalytic activity: Preferential cleavage at the carboxyl of hydro- 3.1 Coverage 7 phobic amino acids, but fails to cleave 15-Leu-—-Tyr-16, 16- 3.2 Known substitutions 7 Tyr-—-Leu-17 and 24-Phe-—-Phe-25 of insulin B chain. Activates 3.3 Surface 7 trypsinogen, and degrades keratin. 3.4 Number of contacts 7 Subcellular location: Secreted. 3.5 Annotation 7 Ptm: O-glycosylated. 3.6 Mutation suggestions 7 Similarity: Belongs to the peptidase A1 family. About: This Swiss-Prot entry is copyright. It is produced through a 4 Appendix 7 collaboration between the Swiss Institute of Bioinformatics and the 4.1 File formats 7 EMBL outstation - the European Bioinformatics Institute. There are 4.2 Color schemes used 8 no restrictions on its use as long as its content is in no way modified 4.3 Credits 8 and this statement is not removed. 1 Lichtarge lab 2006 Fig. 1. Residues 1-167 in 1j71A colored by their relative importance. (See Fig. 2. Residues 168-334 in 1j71A colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Appendix, Fig.9, for the coloring scheme.) 2.2 Multiple sequence alignment for 1j71A For the chain 1j71A, the alignment 1j71A.msf (attached) with 232 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1j71A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 232 Total number of residues: 72780 Smallest: 259 Largest: 334 Average length: 313.7 Alignment length: 334 Average identity: 31% Most related pair: 99% Most unrelated pair: 16% Most distant seq: 30% Furthermore, <1% of residues show as conserved in this ali- Fig. 3. Residues in 1j71A, colored by their relative importance. Clockwise: gnment. front, back, top and bottom views. The alignment consists of 57% eukaryotic ( 14% vertebrata, <1% arthropoda, 40% fungi, <1% plantae) sequences. (Descriptions of some sequences were not readily available.) The file containing the belong to. The clusters in Fig.4 are composed of the residues listed sequence descriptions can be found in the attachment, under the name in Table 1. 1j71A.descr. Table 1. 2.3 Residue ranking in 1j71A cluster size member color residues The 1j71A sequence is shown in Figs. 1–2, with each residue colored red 80 14,21,22,23,25,29,32,33,34 according to its estimated importance. The full listing of residues 35,36,37,38,39,40,65,70,80 in 1j71A can be found in the file called 1j71A.ranks sorted in the 82,84,85,86,92,94,97,109,111 attachment. 112,122,123,124,125,126,127 2.4 Top ranking residues in 1j71A and their position on 128,138,140,141,142,145,151 the structure 156,157,158,159,160,168,170 171,172,173,174,175,176,179 In the following we consider residues ranking among top 25% of resi- 180,182,184,216,217,218,219 dues in the protein . Figure 3 shows residues in 1j71A colored by their 220,221,222,298,299,300,301 importance: bright red and yellow indicate more conserved/important 302,303,304,305,307,308,310 residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. continued in next column 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 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) .(2) A(1)IER 298 I I(65) 0.17 2/0 3.65 L(18) V(10)A T(2)SMY FN 85 G G(60) 0.20 9/9 3.13 V(12) A(13) I(1) L(3)YFD E(1)KSQ TM Table 2. The top 25% of residues in 1j71A at the interface with etha- nol.(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- Fig. 4. Residues in 1j71A, colored according to the cluster they belong to: ber of contacts realized through backbone atoms given in the bracket; dist: red, followed by blue and yellow are the largest clusters (see Appendix for distance of closest apporach to the ligand. ) the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 3. res type disruptive Table 1. continued mutations cluster size member 221 T (R)(K)(H)(FW) color residues 86 D (R)(FWH)(Y)(K) 311,312,319,321 298 I (R)(Y)(H)(K) 85 G (R)(K)(E)(H) Table 1. Clusters of top ranking residues in 1j71A. Table 3. List of disruptive mutations for the top 25% of residues in 1j71A, that are at the interface with ethanol. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier Figure 5 shows residues in 1j71A colored by their importance, at the and the heteroatom name used in that file. interface with 1j71EOH575. Ethanol binding site. Table 2 lists the top 25% of residues at Interface with the peptide 1j71B. Table 4 lists the top 25% the interface with 1j71EOH575 (ethanol). The following table (Table of residues at the interface with 1j71B. The following table (Table 3) suggests possible disruptive replacements for these residues (see 5) suggests possible disruptive replacements for these residues (see Section 3.6). Section 3.6). Table 2. Table 4. res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) 221 T S(18) 0.13 2/0 4.45 34 G G(98)AN 0.01 17/17 3.44 T(73) S A(3) 35 S S(97)TE 0.02 5/2 3.41 G(1)QYV LV FKE 84 Y Y(97).F 0.03 28/17 3.34 86 D D(53) 0.15 7/6 3.86 LQ T(15) 218 D D(96).Q 0.03 11/0 2.69 S(22) GNHS G(1) 221 T S(18) 0.13 1/0 4.17 K(1) continued in next column continued in next column 3 Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) V(15) T(2) F(3). M(3)S Table 4. The top 25% of residues in 1j71A at the interface with 1j71B. (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. ) Table 5. res type disruptive mutations 34 G (R)(KE)(H)(FW) 35 S (R)(K)(H)(FW) 84 Y (K)(Q)(M)(ER) Fig. 5. Residues in 1j71A, at the interface with ethanol, colored by their rela- 218 D (R)(FW)(H)(Y) tive importance. The ligand (ethanol) is colored green. Atoms further than 221 T (R)(K)(H)(FW) 30A˚ away from the geometric center of the ligand, as well as on the line of 82 I (R)(Y)(H)(T) sight to the ligand were removed. (See Appendix for the coloring scheme for 298 I (R)(Y)(H)(K) the protein chain 1j71A.) 85 G (R)(K)(E)(H) 216 V (R)(K)(Y)(E) Table 4. continued res type subst’s cvg noc/ dist Table 5. List of disruptive mutations for the top 25% of residues in 1j71A, that are at the interface with 1j71B.