Pages 1–10 1y75 Evolutionary trace report by report maker January 28, 2010 4 Notes on using trace results 7 4.1 Coverage 7 4.2 Known substitutions 7 4.3 Surface 8 4.4 Number of contacts 8 4.5 Annotation 8 4.6 Mutation suggestions 8 5 Appendix 8 5.1 File formats 8 5.2 Color schemes used 8 5.3 Credits 8 5.3.1 Alistat 8 5.3.2 CE 9 5.3.3 DSSP 9 5.3.4 HSSP 9 5.3.5 LaTex 9 5.3.6 Muscle 9 5.3.7 Pymol 9 5.4 Note about ET Viewer 9 5.5 Citing this work 9 CONTENTS 5.6 About report maker 9 5.7 Attachments 9 1 Introduction 1 2 Chain 1y75A 1 1 INTRODUCTION 2.1 Q5G291 overview 1 From the original Protein Data Bank entry (PDB id 1y75): 2.2 Multiple sequence alignment for 1y75A 1 Title: A new form of catalytically inactive phospholipase a2 with 2.3 Residue ranking in 1y75A 1 an unusual disulphide bridge cys 32- cys 49 reveals recognition for 2.4 Top ranking residues in 1y75A and their position on n-acetylglucosmine the structure 1 Compound: Mol id: 1; molecule: phospholipase a2 isoform 5; chain: 2.4.1 Clustering of residues at 25% coverage. 2 a; ec: 3.1.1.4; mol id: 2; molecule: phospholipase a2 isoform 6; 2.4.2 Overlap with known functional surfaces at chain: b; ec: 3.1.1.4 25% coverage. 3 Organism, scientific name: Naja Sagittifera; 2.4.3 Possible novel functional surfaces at 25% 1y75 contains unique chains 1y75A (118 residues) and 1y75B (118 coverage. 4 residues) 3 Chain 1y75B 5 3.1 Q5G290 overview 5 2 CHAIN 1Y75A 3.2 Multiple sequence alignment for 1y75B 5 3.3 Residue ranking in 1y75B 5 2.1 Q5G291 overview 3.4 Top ranking residues in 1y75B and their position on From SwissProt, id Q5G291, 100% identical to 1y75A: the structure 5 Description: Phospholipase A2 isoform 5 (Fragment). 3.4.1 Clustering of residues at 25% coverage. 5 Organism, scientific name: Naja sagittifera (Andaman cobra). 3.4.2 Overlap with known functional surfaces at Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 25% coverage. 6 Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; 3.4.3 Possible novel functional surfaces at 25% Colubroidea; Elapidae; Elapinae; Naja. coverage. 6 Similarity: Belongs to the phospholipase A2 family. 1 Lichtarge lab 2006 Fig. 1. Residues 1-120 in 1y75A colored by their relative importance. (See Appendix, Fig.12, for the coloring scheme.) 2.2 Multiple sequence alignment for 1y75A For the chain 1y75A, the alignment 1y75A.msf (attached) with 518 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 1y75A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 518 Fig. 2. Residues in 1y75A, colored by their relative importance. Clockwise: Total number of residues: 56626 front, back, top and bottom views. Smallest: 41 Largest: 118 Average length: 109.3 Alignment length: 118 Average identity: 44% Most related pair: 99% Most unrelated pair: 0% Most distant seq: 30% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 62% eukaryotic ( 60% vertebrata, <1% arthropoda, <1% plantae) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1y75A.descr. 2.3 Residue ranking in 1y75A The 1y75A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1y75A can be found in the file called 1y75A.ranks sorted in the attachment. 2.4 Top ranking residues in 1y75A and their position on Fig. 3. Residues in 1y75A, colored according to the cluster they belong to: the structure red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The In the following we consider residues ranking among top 25% of corresponding Pymol script is attached. residues in the protein . Figure 2 shows residues in 1y75A colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A in Table 1. 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 belong to. The clusters in Fig.3 are composed of the residues listed 2 Table 1. cluster size member color residues red 27 5,9,22,25,26,27,28,29,30,33 35,37,39,41,42,44,45,48,49 51,52,68,79,91,93,94,100 blue 2 61,86 Table 1. Clusters of top ranking residues in 1y75A. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Interface with 1y75B.Table 2 lists the top 25% of residues at the interface with 1y75B. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 4.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 30 G G(97)S. 0.06 2/2 4.51 EDNR Fig. 4. Residues in 1y75A, at the interface with 1y75B, colored by their rela- tive importance. 1y75B is shown in backbone representation (See Appendix Table 2. The top 25% of residues in 1y75A at the interface with 1y75B. for the coloring scheme for the protein chain 1y75A.) (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 Table 4. continued contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 22 F Y(87) 0.14 12/10 2.80 Table 3. F(10) res type disruptive .(1)LN mutations 52 Y Y(94)CV 0.17 3/0 4.54 30 G (R)(FW)(KH)(E) .FLSWHA 28 Y H(4) 0.21 5/5 3.50 Table 3. List of disruptive mutations for the top 25% of residues in N(7) 1y75A, that are at the interface with 1y75B. Y(81) F(2) W(3).ES Figure 4 shows residues in 1y75A colored by their importance, at the 5 F F(80) 0.22 33/2 3.42 interface with 1y75B. L(14) NAG binding site. Table 4 lists the top 25% of residues at the inter- .(4)MYE face with 1y75NAG301 (nag). The following table (Table 5) suggests 9 I I(88) 0.24 2/0 3.71 possible disruptive replacements for these residues (see Section 4.6). V(4) Table 4. .(3) res type subst’s cvg noc/ dist antn M(1) (%) bb (A˚ ) L(1)FNW 29 C C(99).A 0.01 15/11 3.65 S-S SA W 49 C D(85) 0.25 3/1 3.96 S-S 30 G G(97)S. 0.06 14/14 3.36 K(5)R EDNR .(1)CH 45 C C(98).R 0.08 12/5 3.72 S-S S(1)G YL N(1)EAQ 48 H H(97).R 0.10 14/2 3.09 M YSQN continued in next column Table 4. The top 25% of residues in 1y75A at the interface with NAG.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each 3 type in the bracket; noc/bb: number of contacts with the ligand, with the num- shows (in blue) the rest of the larger cluster this surface belongs to. ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 5. res type disruptive mutations 29 C (KE)(R)(QD)(MH) 30 G (R)(FW)(KH)(E) 45 C (E)(K)(R)(D) 48 H (E)(T)(MD)(VQA) 22 F (KE)(T)(Q)(D) 52 Y (K)(Q)(E)(M) 28 Y (K)(Q)(M)(ER) Fig. 6. A possible active surface on the chain 1y75A. The larger cluster it 5 F (K)(TE)(QR)(CDG) belongs to is shown in blue. 9 I (R)(Y)(T)(H) 49 C (R)(E)(FW)(KH) The residues belonging to this surface ”patch” are listed in Table Table 5. List of disruptive mutations for the top 25% of residues in 6, while Table 7 suggests possible disruptive replacements for these 1y75A, that are at the interface with NAG. residues (see Section 4.6). Table 6. res type substitutions(%) cvg antn 29 C C(99).AW 0.01 S-S 39 D D(98).QREPG 0.02 27 C C(96)R.N(2)KDE 0.03 S-S 51 C C(99).F 0.04 S-S 26 G G(98).FASL 0.05 30 G G(97)S.EDNR 0.06 45 C C(98).RYL 0.08 S-S 33 G G(98).PRNSKA 0.09 44 C C(98).ATYWG 0.09 S-S 48 H H(97).RYSQN 0.10 68 Y Y(94)F.(1)CSLRI 0.12 AHG 22 F Y(87)F(10).(1)L 0.14 N 35 G G(93)KR(2).ENQL 0.14 HIPASD 93 C C(96).(2)AYL 0.15 S-S 37 P P(95).A(2)TRKIG 0.16 Y 52 Y Y(94)CV.FLSWHA 0.17 100 C C(95).(3)RYV 0.18 S-S 28 Y H(4)N(7)Y(81) 0.21 F(2)W(3).ES Fig.