Pages 1–8 1sl8 Evolutionary trace report by report maker June 25, 2009 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 1sl8): Title: Calcium-loaded apo-aequorin from aequorea victoria Compound: Mol id: 1; molecule: aequorin 1; chain: a; engineered: yes Organism, scientific name: Aequorea Victoria; 1sl8 contains a single unique chain 1sl8A (181 residues long). 2 CHAIN 1SL8A CONTENTS 2.1 P07164 overview 1 Introduction 1 From SwissProt, id P07164, 99% identical to 1sl8A: Description: Aequorin-1 precursor. 2 Chain 1sl8A 1 Organism, scientific name: Aequorea victoria (Jellyfish). 2.1 P07164 overview 1 Taxonomy: Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; 2.2 Multiple sequence alignment for 1sl8A 1 Leptomedusae; Aequoreidae; Aequorea. 2.3 Residue ranking in 1sl8A 1 Function: Ca(2+)-dependent bioluminescence photoprotein. Dis- 2.4 Top ranking residues in 1sl8A and their position on plays an emission peak at 470 nm (blue light). Trace amounts of the structure 1 calcium ion trigger the intramolecular oxidation of the chromophore, 2.4.1 Clustering of residues at 25% coverage. 2 coelenterazine into coelenteramide and CO(2) with the concomitant 2.4.2 Overlap with known functional surfaces at emission of light. 25% coverage. 2 Ptm: The reduction of the disulfide bond is necessary to regenerate 2.4.3 Possible novel functional surfaces at 25% aequorin from apoaequorin. coverage. 4 Biotechnology: Aequorin is used as an intracellular Ca(2+) indicator. Aequorin has a number of advantages over other Ca(2+) indica- 3 Notes on using trace results 6 tors, for example, low leakage rate from cells, lack of intracellular 3.1 Coverage 6 compartmentalization or sequestration and it does not disrupt cell 3.2 Known substitutions 6 functions or embryo development. 3.3 Surface 6 Similarity: Belongs to the aequorin family. 3.4 Number of contacts 6 Similarity: Contains 4 EF-hand domains. 3.5 Annotation 6 Caution: Was originally (Ref.4) thought to have a internal disulfide 3.6 Mutation suggestions 6 bond. About: This Swiss-Prot entry is copyright. It is produced through a 4 Appendix 6 collaboration between the Swiss Institute of Bioinformatics and the 4.1 File formats 6 EMBL outstation - the European Bioinformatics Institute. There are 4.2 Color schemes used 6 no restrictions on its use as long as its content is in no way modified 4.3 Credits 6 and this statement is not removed. 1 Lichtarge lab 2006 Fig. 1. Residues 11-191 in 1sl8A colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) 2.2 Multiple sequence alignment for 1sl8A For the chain 1sl8A, the alignment 1sl8A.msf (attached) with 34 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 1sl8A.msf. Its statistics, from the alistat program are the following: Fig. 2. Residues in 1sl8A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 34 Total number of residues: 5224 Smallest: 136 Largest: 181 Average length: 153.6 Alignment length: 181 Average identity: 54% Most related pair: 99% Most unrelated pair: 23% Most distant seq: 48% Furthermore, 6% of residues show as conserved in this alignment. The alignment consists of 44% eukaryotic ( 2% vertebrata, 5% fungi, 8% 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 1sl8A.descr. 2.3 Residue ranking in 1sl8A The 1sl8A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1sl8A can be found in the file called 1sl8A.ranks sorted in the attachment. 2.4 Top ranking residues in 1sl8A and their position on Fig. 3. Residues in 1sl8A, 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 resi- corresponding Pymol script is attached. dues in the protein . Figure 2 shows residues in 1sl8A 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. 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 in Table 1. 2 Table 1. cluster size member color residues red 24 46,50,59,60,115,117,119,120 121,124,126,128,132,134,146 150,151,154,155,157,159,160 166,167 blue 18 14,17,18,19,21,22,25,26,28 31,33,37,65,66,67,81,84,88 yellow 2 139,140 Table 1. Clusters of top ranking residues in 1sl8A. 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. Calcium ion binding site. Table 2 lists the top 25% of residues at the interface with 1sl8CA670 (calcium ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Fig. 4. Residues in 1sl8A, at the interface with calcium ion, colored by their res type subst’s cvg noc/ dist relative importance. The ligand (calcium ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line (%) bb (A˚ ) of sight to the ligand were removed. (See Appendix for the coloring scheme 31 G G(100) 0.07 1/1 4.77 for the protein chain 1sl8A.) 33 I I(100) 0.07 2/2 4.25 37 E E(100) 0.07 4/0 2.43 26 D D(97) 0.08 7/3 2.16 (Table 5) suggests possible disruptive replacements for these residues Q(2) (see Section 3.6). 28 N D(55) 0.21 7/3 2.36 N(41) Table 4. A(2) res type subst’s cvg noc/ dist (%) bb (A˚ ) Table 2. The top 25% of residues in 1sl8A at the interface with calcium 120 K K(100) 0.07 1/1 4.72 ion.(Field names: res: residue number in the PDB entry; type: amino acid 124 G G(100) 0.07 1/1 4.86 type; substs: substitutions seen in the alignment; with the percentage of each 121 D D(97) 0.08 7/3 2.27 type in the bracket; noc/bb: number of contacts with the ligand, with the num- N(2) ber of contacts realized through backbone atoms given in the bracket; dist: 126 I I(97) 0.09 3/3 4.36 distance of closest apporach to the ligand. ) V(2) 119 D D(97) 0.13 7/3 2.24 G(2) Table 3. res type disruptive Table 4. The top 25% of residues in 1sl8A at the interface with calcium mutations ion.(Field names: res: residue number in the PDB entry; type: amino acid 31 G (KER)(FQMWHD)(NYLPI)(SVA) 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- 33 I (YR)(TH)(SKECG)(FQWD) ber of contacts realized through backbone atoms given in the bracket; dist: 37 E (FWH)(YVCARG)(T)(SNKLPI) distance of closest apporach to the ligand. ) 26 D (FWHR)(Y)(VCAG)(T) 28 N (Y)(H)(FW)(R) Table 5. Table 3. List of disruptive mutations for the top 25% of residues in 1sl8A, res type disruptive that are at the interface with calcium ion. mutations 120 K (Y)(FTW)(SVCAG)(HD) Figure 4 shows residues in 1sl8A colored by their importance, at the 124 G (KER)(FQMWHD)(NYLPI)(SVA) interface with 1sl8CA670. 121 D (R)(FWH)(Y)(VCAG) Calcium ion binding site. Table 4 lists the top 25% of residues continued in next column at the interface with 1sl8CA671 (calcium ion). The following table 3 Table 5. continued Table 6. continued res type disruptive res type subst’s cvg noc/ dist mutations (%) bb (A˚ ) 126 I (YR)(H)(TKE)(SQCDG) S(35) 119 D (R)(FWH)(K)(Y) Table 6. The top 25% of residues in 1sl8A at the interface with calcium Table 5. List of disruptive mutations for the top 25% of residues in 1sl8A, ion.(Field names: res: residue number in the PDB entry; type: amino acid that are at the interface with calcium ion. 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. ) Table 7. res type disruptive mutations 155 D (R)(FWH)(KYVCAG)(TQM) 160 G (KER)(FQMWHD)(NYLPI)(SVA) 157 D (R)(FWH)(Y)(VCAG) 166 E (FWH)(R)(Y)(VA) 159 S (R)(K)(FWH)(QM) Table 7.