1Mh2 Lichtarge Lab 2006

Pages 1–10 1mh2 Evolutionary trace report by report maker July 21, 2010 4 Notes on using trace results 7 4.1 Coverage 7 4.2 Known substitutions 8 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 9 5.3 Credits 9 5.3.1 Alistat 9 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 5.6 About report maker 9 CONTENTS 5.7 Attachments 9 1 Introduction 1 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1mh2): 2 Chain 1mh2A 1 Title: Crystal structure of a zinc containing dimer of phospholipase 2.1 P60043 overview 1 a2 from the venom of indian cobra (naja naja sagittifera) 2.2 Multiple sequence alignment for 1mh2A 1 Compound: Mol id: 1; molecule: phospholipase a2; chain: a; ec: 2.3 Residue ranking in 1mh2A 1 3.1.1.4; mol id: 2; molecule: phospholipase a2; chain: b; ec: 3.1.1.4 2.4 Top ranking residues in 1mh2A and their position on Organism, scientific name: Naja Sagittifera; the structure 1 1mh2 contains unique chains 1mh2A (119 residues) and 1mh2B 2.4.1 Clustering of residues at 25% coverage. 2 (119 residues) 2.4.2 Overlap with known functional surfaces at 25% coverage. 2 2 CHAIN 1MH2A 2.4.3 Possible novel functional surfaces at 25% coverage. 3 2.1 P60043 overview From SwissProt, id P60043, 93% identical to 1mh2A: 3 Chain 1mh2B 4 Description: Phospholipase A2 isoform 1 precursor (EC 3.1.1.4) 3.1 P60044 overview 4 (Phosphatidylcholine 2-acylhydrolase) (Fragment). 3.2 Multiple sequence alignment for 1mh2B 5 Organism, scientific name: Naja sagittifera (Andaman cobra). 3.3 Residue ranking in 1mh2B 5 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 3.4 Top ranking residues in 1mh2B and their position on Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; the structure 5 Colubroidea; Elapidae; Elapinae; Naja. 3.4.1 Clustering of residues at 25% coverage. 5 Function: PA2 catalyzes the calcium-dependent hydrolysis of the 2- 3.4.2 Overlap with known functional surfaces at acyl groups in 3-sn-phosphoglycerides. 25% coverage. 6 Catalytic activity: Phosphatidylcholine + H(2)O = 1- acylglycero- 3.4.3 Possible novel functional surfaces at 25% phosphocholine + a carboxylate. coverage. 6 Cofactor: Binds 1 calcium ion per subunit (By similarity). 1 Lichtarge lab 2006 2.4 Top ranking residues in 1mh2A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 1mh2A 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 1-120 in 1mh2A colored by their relative importance. (See Appendix, Fig.12, for the coloring scheme.) Subunit: Heterodimer formed between two homologous isoforms: isoform 1 and isoform 2. Subcellular location: Secreted. Similarity: Belongs to the phospholipase A2 family. Group I subfa- mily. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are 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 1mh2A For the chain 1mh2A, the alignment 1mh2A.msf (attached) with 538 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 1mh2A.msf. Its statistics, from the alistat program are the following: Fig. 2. Residues in 1mh2A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 538 Total number of residues: 58778 Smallest: 42 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the Largest: 119 top 25% of all residues, this time colored according to clusters they Average length: 109.3 belong to. The clusters in Fig.3 are composed of the residues listed Alignment length: 119 in Table 1. Average identity: 43% Most related pair: 99% Table 1. Most unrelated pair: 0% cluster size member Most distant seq: 32% color residues red 27 2,5,8,9,22,25,26,27,28,29,30 35,37,39,41,42,44,45,48,51 Furthermore, <1% of residues show as conserved in this ali- 52,68,79,91,93,94,100 gnment. blue 2 61,86 The alignment consists of 61% eukaryotic ( 59% vertebrata, <1% arthropoda, <1% plantae), and <1% prokaryotic sequences. (Des- Table 1. Clusters of top ranking residues in 1mh2A. criptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1mh2A.descr. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier 2.3 Residue ranking in 1mh2A and the heteroatom name used in that file. Interface with 1mh2B.Table 2 lists the top 25% of residues at The 1mh2A sequence is shown in Fig. 1, with each residue colored the interface with 1mh2B. The following table (Table 3) suggests according to its estimated importance. The full listing of residues in possible disruptive replacements for these residues (see Section 4.6). 1mh2A can be found in the file called 1mh2A.ranks sorted in the attachment. 2 Fig. 3. Residues in 1mh2A, colored according to the cluster they belong to: Fig. 4. Residues in 1mh2A, at the interface with 1mh2B, colored by their rela- red, followed by blue and yellow are the largest clusters (see Appendix for tive importance. 1mh2B is shown in backbone representation (See Appendix the coloring scheme). Clockwise: front, back, top and bottom views. The for the coloring scheme for the protein chain 1mh2A.) corresponding Pymol script is attached. Acetic acid binding site. Table 4 lists the top 25% of residues Table 2. at the interface with 1mh2ACY302 (acetic acid). The following table res type subst’s cvg noc/ dist (Table 5) suggests possible disruptive replacements for these residues (%) bb (A˚ ) (see Section 4.6). 30 G G(96)NL 0.06 2/2 4.25 Table 4. S(1).VT res type subst’s cvg noc/ dist antn RD (%) bb (A˚ ) 32 G G(92)S. 0.10 18/18 3.18 30 G G(96)NL 0.06 1/1 4.89 L(2) S(1).VT E(1)VAN RD KQIRM 45 C C(96)SE 0.09 1/1 4.32 S-S K.DAYRQ Table 2. The top 25% of residues in 1mh2A at the interface with 1mh2B. 48 H H(95)PQ 0.13 16/4 2.48 (Field names: res: residue number in the PDB entry; type: amino acid type; .LRYSVT substs: substitutions seen in the alignment; with the percentage of each type INGE in the bracket; noc/bb: number of contacts with the ligand, with the number of 52 Y Y(91)DT 0.22 6/0 4.42 contacts realized through backbone atoms given in the bracket; dist: distance CV(2) of closest apporach to the ligand. ) F(1) .(1)HLS WIP Table 3. res type disruptive Table 4. The top 25% of residues in 1mh2A at the interface with acetic mutations acid.(Field names: res: residue number in the PDB entry; type: amino acid 30 G (R)(K)(E)(H) type; substs: substitutions seen in the alignment; with the percentage of each 32 G (R)(EH)(Y)(FKW) 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 3. List of disruptive mutations for the top 25% of residues in 1mh2A, that are at the interface with 1mh2B. Figure 4 shows residues in 1mh2A colored by their importance, at the interface with 1mh2B. 3 Table 5. res type disruptive mutations 30 G (R)(K)(E)(H) 45 C (R)(FKW)(EH)(M) 48 H (E)(TD)(Q)(M) 52 Y (K)(Q)(R)(M) Table 5. List of disruptive mutations for the top 25% of residues in 1mh2A, that are at the interface with acetic acid. Fig. 6. A possible active surface on the chain 1mh2A. The larger cluster it belongs to is shown in blue. Table 6. continued res type substitutions(%) cvg antn 51 C C(98).PF 0.03 S-S 35 G G(95)Q.AR(1) 0.04 H(1)EPND 44 C C(97).AVPYWG 0.05 S-S 30 G G(96)NLS(1).VTR 0.06 D 26 G G(95)TR.DSALCN 0.08 39 D D(96)T.(1)KVENG 0.08 45 C C(96)SEK.DAYRQ 0.09 S-S 32 G G(92)S.L(2)E(1) 0.10 VANKQIRM 48 H H(95)PQ.LRYSVTI 0.13 NGE 68 Y Y(93)FR.(2)CSIA 0.13 LM 5 F F(77).(7)L(14)M 0.14 YIE 100 C C(92).(6)NGRYK 0.15 S-S Fig. 5. Residues in 1mh2A, at the interface with acetic acid, colored by their 22 F Y(83)I.(3)F(11) 0.18 relative importance.

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