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1Ls9 Lichtarge Lab 2006 Pages 1–6 1ls9 Evolutionary trace report by report maker September 26, 2008 4.3.1 Alistat 5 4.3.2 CE 5 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ls9): Title: Structure of the cytochrome c6 from the green alga cladophora glomerata Compound: Mol id: 1; molecule: cytochrome c6; chain: a Organism, scientific name: Cladophora Glomerata 1ls9 contains a single unique chain 1ls9A (91 residues long). 2 CHAIN 1LS9A CONTENTS 2.1 P83391 overview 1 Introduction 1 From SwissProt, id P83391, 100% identical to 1ls9A: Description: Cytochrome c6 (Soluble cytochrome f) (Cytochrome 2 Chain 1ls9A 1 c553) (Cytochrome c- 553). 2.1 P83391 overview 1 Organism, scientific name: Cladophora glomerata. 2.2 Multiple sequence alignment for 1ls9A 1 Taxonomy: Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; 2.3 Residue ranking in 1ls9A 1 Cladophorales; Cladophoraceae; Cladophora. 2.4 Top ranking residues in 1ls9A and their position on Function: Functions as an electron carrier between membrane- the structure 1 bound cytochrome b6f and photosystem I in oxygenic photosynthesis 2.4.1 Clustering of residues at 25% coverage. 2 (By similarity). 2.4.2 Overlap with known functional surfaces at Subunit: Monomer. 25% coverage. 2 Subcellular location: Chloroplast; within the thylakoid lumen. 2.4.3 Possible novel functional surfaces at 25% Ptm: Binds 1 heme group per subunit. coverage. 3 Similarity: Belongs to the cytochrome c family. PetJ subfamily. About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 4 collaboration between the Swiss Institute of Bioinformatics and the 3.1 Coverage 4 EMBL outstation - the European Bioinformatics Institute. There are 3.2 Known substitutions 4 no restrictions on its use as long as its content is in no way modified 3.3 Surface 4 and this statement is not removed. 3.4 Number of contacts 4 2.2 Multiple sequence alignment for 1ls9A 3.5 Annotation 4 3.6 Mutation suggestions 4 For the chain 1ls9A, the alignment 1ls9A.msf (attached) with 28 sequences was used. The alignment was assembled through combi- 4 Appendix 5 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 5 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 5 report, under the name of 1ls9A.msf. Its statistics, from the alistat 4.3 Credits 5 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-91 in 1ls9A colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Format: MSF Number of sequences: 28 Total number of residues: 2459 Smallest: 81 Largest: 91 Average length: 87.8 Alignment length: 91 Average identity: 54% Most related pair: 99% Most unrelated pair: 35% Most distant seq: 56% Furthermore, 9% of residues show as conserved in this alignment. Fig. 2. Residues in 1ls9A, colored by their relative importance. Clockwise: The alignment consists of 46% eukaryotic ( 14% plantae), and front, back, top and bottom views. 50% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1ls9A.descr. 2.3 Residue ranking in 1ls9A The 1ls9A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1ls9A can be found in the file called 1ls9A.ranks sorted in the attachment. 2.4 Top ranking residues in 1ls9A and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 1ls9A 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. Table 1. cluster size member Fig. 3. Residues in 1ls9A, colored according to the cluster they belong to: color residues red, followed by blue and yellow are the largest clusters (see Appendix for red 23 9,13,16,17,18,20,21,24,26,33 the coloring scheme). Clockwise: front, back, top and bottom views. The 34,55,56,59,62,63,64,70,75 corresponding Pymol script is attached. 78,81,82,91 HEM binding site. Table 2 lists the top 25% of residues at the Table 1. Clusters of top ranking residues in 1ls9A. interface with 1ls9AHEM92 (hem). The following table (Table 3) suggests possible disruptive replacements for these residues (see 2.4.2 Overlap with known functional surfaces at 25% coverage. Section 3.6). The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. 2 Table 2. Table 3. continued res type subst’s cvg noc/ dist res type disruptive (%) bb (A˚ ) mutations 13 F F(100) 0.10 2/0 4.66 70 L (YR)(TH)(SKECG)(FQWD) 17 C C(100) 0.10 39/21 1.81 33 T (R)(K)(H)(FW) 34 L L(100) 0.10 20/3 3.41 62 A (Y)(R)(E)(H) 63 M M(100) 0.10 91/23 2.28 82 V (YR)(KE)(H)(QD) 78 V V(100) 0.10 7/1 3.91 26 N (FWH)(Y)(R)(E) 20 C C(96) 0.13 27/8 1.91 56 V (YR)(KE)(H)(QD) A(3) 55 Q (Y)(H)(T)(FW) 21 H H(96) 0.13 79/0 1.99 T(3) Table 3. List of disruptive mutations for the top 25% of residues in 1ls9A, 16 N N(92) 0.15 15/13 3.44 that are at the interface with HEM. H(7) 64 P P(92) 0.15 22/4 3.64 S(7) 70 L L(96) 0.18 1/0 4.25 I(3) 33 T T(85) 0.20 14/14 2.62 N(7) V(7) 62 A A(85) 0.20 18/17 3.81 N(7) P(7) 82 V V(96) 0.21 3/0 3.88 I(3) 26 N N(92) 0.22 22/0 3.19 T(3) G(3) 56 V V(92) 0.23 10/0 3.61 L(3) I(3) 55 Q Q(92) 0.24 25/0 3.31 L(3) I(3) Table 2. The top 25% of residues in 1ls9A at the interface with HEM.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each Fig. 4. Residues in 1ls9A, at the interface with HEM, colored by their relative A type in the bracket; noc/bb: number of contacts with the ligand, with the num- importance. The ligand (HEM) is colored green. Atoms further than 30 ˚ ber of contacts realized through backbone atoms given in the bracket; dist: away from the geometric center of the ligand, as well as on the line of sight distance of closest apporach to the ligand. ) to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1ls9A.) Table 3. res type disruptive Figure 4 shows residues in 1ls9A colored by their importance, at the mutations interface with 1ls9AHEM92. 13 F (KE)(TQD)(SNCRG)(M) 2.4.3 Possible novel functional surfaces at 25% coverage. One 17 C (KER)(FQMWHD)(NYLPI)(SVA) group of residues is conserved on the 1ls9A surface, away from (or 34 L (YR)(TH)(SKECG)(FQWD) susbtantially larger than) other functional sites and interfaces reco- 63 M (Y)(TH)(SCRG)(FWD) gnizable in PDB entry 1ls9. It is shown in Fig. 5. The residues 78 V (KYER)(QHD)(N)(FTMW) belonging to this surface ”patch” are listed in Table 4, while Table 20 C (KER)(QHD)(FYMW)(N) 5 suggests possible disruptive replacements for these residues (see 21 H (E)(QM)(KD)(NLPI) Section 3.6). 16 N (TY)(E)(SFVCAWG)(MHDR) 64 P (R)(Y)(H)(K) continued in next column 3 Table 5. continued res type disruptive mutations 34 L (YR)(TH)(SKECG)(FQWD) 59 G (KER)(FQMWHD)(NYLPI)(SVA) 63 M (Y)(TH)(SCRG)(FWD) 78 V (KYER)(QHD)(N)(FTMW) 81 Y (K)(QM)(NEVLAPIR)(D) 91 W (KE)(TQD)(SNCRG)(M) 20 C (KER)(QHD)(FYMW)(N) 21 H (E)(QM)(KD)(NLPI) 16 N (TY)(E)(SFVCAWG)(MHDR) 64 P (R)(Y)(H)(K) 70 L (YR)(TH)(SKECG)(FQWD) 75 I (Y)(R)(TH)(SCG) 33 T (R)(K)(H)(FW) 62 A (Y)(R)(E)(H) 82 V (YR)(KE)(H)(QD) 26 N (FWH)(Y)(R)(E) 56 V (YR)(KE)(H)(QD) 55 Q (Y)(H)(T)(FW) 18 A (R)(KY)(E)(H) Fig. 5. A possible active surface on the chain 1ls9A. Table 5. Disruptive mutations for the surface patch in 1ls9A. Table 4. res type substitutions(%) cvg 13 F F(100) 0.10 3 NOTES ON USING TRACE RESULTS 17 C C(100) 0.10 34 L L(100) 0.10 3.1 Coverage 59 G G(100) 0.10 Trace results are commonly expressed in terms of coverage: the resi- 63 M M(100) 0.10 due is important if its “coverage” is small - that is if it belongs to 78 V V(100) 0.10 some small top percentage of residues [100% is all of the residues 81 Y Y(100) 0.10 in a chain], according to trace.
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