Pages 1–8 2aip Evolutionary trace report by report maker October 9, 2009 4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 7 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 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2aip): Title: Crystal structure of native protein c activator from the venom of copperhead snake agkistrodon contortrix contortrix Compound: Mol id: 1; molecule: protein c activator; chain: a; synonym: venombin a, ancrod, acc-c; ec: 3.4.21.74 Organism, scientific name: Agkistrodon Contortrix Contortrix; 2aip contains a single unique chain 2aipA (231 residues long). CONTENTS 2 CHAIN 2AIPA 1 Introduction 1 2.1 P09872 overview 2 Chain 2aipA 1 From SwissProt, id P09872, 100% identical to 2aipA: 2.1 P09872 overview 1 Description: Ancrod (EC 3.4.21.74) (Venombin A) (Protein C 2.2 Multiple sequence alignment for 2aipA 1 activator) (ACC-C). 2.3 Residue ranking in 2aipA 1 Organism, scientific name: Agkistrodon contortrix contortrix 2.4 Top ranking residues in 2aipA and their position on (Southern copperhead). the structure 1 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 2.4.1 Clustering of residues at 25% coverage. 2 Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; 2.4.2 Overlap with known functional surfaces at Colubroidea; Viperidae; Crotalinae; Agkistrodon. 25% coverage. 2 Function: Thrombin-like snake venom serine protease. Cleaves 2.4.3 Possible novel functional surfaces at 25% fibrinopeptides AM, AO, and AY; the aberrant fibrinogen is then coverage. 5 incapable of being cross-linked, forming easily dispersible clots. Activates protein C. 3 Notes on using trace results 6 Catalytic activity: Selective cleavage of Arg-—-Xaa bond in fibri- 3.1 Coverage 6 nogen, to form fibrin, and release fibrinopeptide A. The specificity 3.2 Known substitutions 6 of further degradation of fibrinogen varies with species origin of the 3.3 Surface 6 enzyme. 3.4 Number of contacts 6 Subcellular location: Secreted (Potential). 3.5 Annotation 7 Tissue specificity: Expressed by the venom gland. 3.6 Mutation suggestions 7 Similarity: Belongs to the peptidase S1 family. Snake venom subfamily. 4 Appendix 7 Similarity: Contains 1 peptidase S1 domain. 4.1 File formats 7 About: This Swiss-Prot entry is copyright. It is produced through a 4.2 Color schemes used 7 collaboration between the Swiss Institute of Bioinformatics and the 4.3 Credits 7 EMBL outstation - the European Bioinformatics Institute. There are 1 Lichtarge lab 2006 Fig. 1. Residues 16-134 in 2aipA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Note that some residues in 2aipA carry insertion code. Fig. 2. Residues 135-245 in 2aipA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Note that some residues in 2aipA carry insertion code. no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Multiple sequence alignment for 2aipA For the chain 2aipA, the alignment 2aipA.msf (attached) with 1080 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 2aipA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 1080 Total number of residues: 238093 Smallest: 174 Largest: 231 Average length: 220.5 Alignment length: 231 Average identity: 35% Most related pair: 99% Most unrelated pair: 15% Most distant seq: 37% Fig. 3. Residues in 2aipA, colored by their relative importance. Clockwise: Furthermore, <1% of residues show as conserved in this ali- front, back, top and bottom views. gnment. The alignment consists of 49% eukaryotic ( 38% vertebrata, 10% arthropoda, <1% fungi), <1% prokaryotic, and <1% viral 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the sequences. (Descriptions of some sequences were not readily availa- top 25% of all residues, this time colored according to clusters they ble.) The file containing the sequence descriptions can be found in belong to. The clusters in Fig.4 are composed of the residues listed the attachment, under the name 2aipA.descr. in Table 1. Table 1. 2.3 Residue ranking in 2aipA cluster size member The 2aipA sequence is shown in Figs. 1–2, with each residue colored color residues according to its estimated importance. The full listing of residues red 54 42,43,44,46,51,52,54,55,56 in 2aipA can be found in the file called 2aipA.ranks sorted in the 57,58,102,103,104,105,108 attachment. 123,124,136,139,140,141,142 155,168,180,182,183,184,186 2.4 Top ranking residues in 2aipA and their position on 189,191,193,194,195,196,197 the structure 198,199,211,213,214,215,216 220,221,225,226,227,228,229 In the following we consider residues ranking among top 25% of resi- 231,237,238 dues in the protein . Figure 3 shows residues in 2aipA colored by their importance: bright red and yellow indicate more conserved/important continued in next column residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2 Table 3. res type disruptive mutations 91 C (KER)(Q)(MD)(FWH) 237 W (K)(E)(Q)(D) Table 3. List of disruptive mutations for the top 25% of residues in 2aipA, that are at the interface with sulfate ion. Fig. 4. Residues in 2aipA, 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. Table 1. continued cluster size member color residues blue 2 18,19 Table 1. Clusters of top ranking residues in 2aipA. Fig. 5. Residues in 2aipA, at the interface with sulfate ion, colored by their relative importance. The ligand (sulfate ion) 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 2.4.2 Overlap with known functional surfaces at 25% coverage. for the protein chain 2aipA.) The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Sulfate ion binding site. Table 2 lists the top 25% of residues at the Figure 5 shows residues in 2aipA colored by their importance, at the interface with 2aipSO4303 (sulfate ion). The following table (Table interface with 2aipSO4303. 3) suggests possible disruptive replacements for these residues (see Sulfate ion binding site. Table 4 lists the top 25% of residues at the Section 3.6). interface with 2aipSO4301 (sulfate ion). The following table (Table 5) suggests possible disruptive replacements for these residues (see Table 2. Section 3.6). res type subst’s cvg noc/ dist antn Table 4. A˚ (%) bb ( ) res type subst’s cvg noc/ dist antn 91 C 228.(2) 0.03 15/10 3.32 S-S (%) bb (A˚ ) 35 194 D D(99)EV 0.01 3/3 4.05 237 W W(95) 0.08 1/0 4.77 . F(2)Y 42 C C(98)WV 0.03 1/0 4.30 S-S .(1)CSV .GA 58 C C(98)L. 0.03 1/0 5.00 S-S Table 2. The top 25% of residues in 2aipA at the interface with sulfate NVSA ion.(Field names: res: residue number in the PDB entry; type: amino acid 191 C C(96) 0.04 2/2 4.04 S-S 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- continued in next column ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 3 Table 4. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) F(2)YSG .A 195 S S(98)NG 0.05 14/5 2.87 FYPA. 57 H H(97)AR 0.07 12/0 2.75 QN.LSP 193 G G(92) 0.09 9/9 2.96 A(1) R(1)VSM QDYEFCH T. Table 4. The top 25% of residues in 2aipA at the interface with sulfate ion.(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. ) Fig. 6. Residues in 2aipA, at the interface with sulfate ion, colored by their Table 5. relative importance. The ligand (sulfate ion) is colored green. Atoms further res type disruptive than 30A˚ away from the geometric center of the ligand, as well as on the line mutations of sight to the ligand were removed. (See Appendix for the coloring scheme 194 D (R)(H)(FW)(Y) for the protein chain 2aipA.) 42 C (K)(E)(R)(Q) 58 C (R)(K)(E)(H) 191 C (K)(R)(E)(Q) 195 S (KR)(Q)(H)(EM) 57 H (E)(T)(D)(Q) 193 G (KR)(E)(H)(Q) Table 5.