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1A2s Lichtarge Lab 2006 Pages 1–6 1a2s Evolutionary trace report by report maker June 19, 2010 4.3.1 Alistat 5 4.3.2 CE 5 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 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 1a2s): Title: The solution nmr structure of oxidized cytochrome c6 from the green alga monoraphidium braunii, minimized average structure Compound: Mol id: 1; molecule: cytochrome c6; chain: a; synonym: cytochrome c552; other details: oxidized form Organism, scientific name: Monoraphidium Braunii; 1a2s contains a single unique chain 1a2sA (89 residues long). This CONTENTS is an NMR-determined structure – in this report the first model in the 1 Introduction 1 file was used. 2 Chain 1a2sA 1 2.1 Q09099 overview 1 2 CHAIN 1A2SA 2.2 Multiple sequence alignment for 1a2sA 1 2.1 Q09099 overview 2.3 Residue ranking in 1a2sA 1 2.4 Top ranking residues in 1a2sA and their position on From SwissProt, id Q09099, 85% identical to 1a2sA: the structure 2 Description: Cytochrome c6 (Soluble cytochrome f) (Cytochrome 2.4.1 Clustering of residues at 25% coverage. 2 c553) (Cytochrome c- 553) (Cytochrome c-552). 2.4.2 Overlap with known functional surfaces at Organism, scientific name: Monoraphidium braunii. 25% coverage. 2 Taxonomy: Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; 2.4.3 Possible novel functional surfaces at 25% Sphaeropleales; Selenastraceae; Monoraphidium. coverage. 3 Function: Functions as an electron carrier between membrane- bound cytochrome b6f and photosystem I in oxygenic photosynthe- 3 Notes on using trace results 4 sis. 3.1 Coverage 4 Biophysicochemical properties: 3.2 Known substitutions 4 Redox potential: E(0) is +358 mV; 3.3 Surface 4 Subunit: Monomer. 3.4 Number of contacts 4 Subcellular location: Chloroplast; within the thylakoid lumen. 3.5 Annotation 5 Ptm: Binds 1 heme group per subunit. 3.6 Mutation suggestions 5 Similarity: Belongs to the cytochrome c family. PetJ subfamily. About: This Swiss-Prot entry is copyright. It is produced through a 4 Appendix 5 collaboration between the Swiss Institute of Bioinformatics and the 4.1 File formats 5 EMBL outstation - the European Bioinformatics Institute. There are 4.2 Color schemes used 5 no restrictions on its use as long as its content is in no way modified 4.3 Credits 5 and this statement is not removed. 1 Lichtarge lab 2006 Fig. 1. Residues 1-89 in 1a2sA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) 2.2 Multiple sequence alignment for 1a2sA For the chain 1a2sA, the alignment 1a2sA.msf (attached) with 110 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 1a2sA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 110 Total number of residues: 9218 Smallest: 72 Largest: 89 Fig. 2. Residues in 1a2sA, colored by their relative importance. Clockwise: Average length: 83.8 front, back, top and bottom views. Alignment length: 89 Average identity: 45% Most related pair: 99% Most unrelated pair: 14% Most distant seq: 33% Furthermore, 2% of residues show as conserved in this alignment. The alignment consists of 22% eukaryotic ( 7% plantae), and 19% 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 1a2sA.descr. 2.3 Residue ranking in 1a2sA The 1a2sA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1a2sA can be found in the file called 1a2sA.ranks sorted in the attachment. 2.4 Top ranking residues in 1a2sA 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 1a2sA colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for Fig. 3. Residues in 1a2sA, colored according to the cluster they belong to: producing this figure can be found in the attachment. red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the corresponding Pymol script is attached. 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 color residues continued in next column 2 Table 1. continued Table 2. continued cluster size member res type subst’s cvg noc/ dist color residues (%) bb (A˚ ) red 22 7,11,14,15,18,19,22,32,50,53 T(4)V 57,59,60,61,62,64,68,73,76 60 A A(69) 0.23 86/43 2.39 77,79,80 G(5) N(8) Table 1. Clusters of top ranking residues in 1a2sA. V(10) P(2)SME K 2.4.2 Overlap with known functional surfaces at 25% coverage. 50 I I(89) 0.24 53/1 2.29 The name of the ligand is composed of the source PDB identifier L(2) and the heteroatom name used in that file. V(7)Y Heme c binding site. Table 2 lists the top 25% of residues at 32 L L(88). 0.25 122/1 2.40 the interface with 1a2sHEC19 (heme c). The following table (Table V(1)IA 3) suggests possible disruptive replacements for these residues (see Q(2) Section 3.6). G(1)PDM Table 2. Table 2. The top 25% of residues in 1a2sA at the interface with heme res type subst’s cvg noc/ dist c.(Field names: res: residue number in the PDB entry; type: amino acid type; ˚ (%) bb (A) substs: substitutions seen in the alignment; with the percentage of each type 15 C C(100) 0.02 118/37 1.82 in the bracket; noc/bb: number of contacts with the ligand, with the number of 61 M M(100) 0.02 205/19 2.44 contacts realized through backbone atoms given in the bracket; dist: distance 68 L L(98)IV 0.03 35/0 2.56 of closest apporach to the ligand. ) 18 C C(99)A 0.06 92/13 1.83 19 H H(99)T 0.06 136/0 1.98 62 P P(91) 0.08 95/1 2.27 Table 3. S(7)T res type disruptive 80 V V(96)L 0.09 50/0 2.36 mutations I(2) 15 C (KER)(FQMWHD)(NYLPI)(SVA) 11 F F(96)V 0.10 17/0 3.54 61 M (Y)(TH)(SCRG)(FWD) Y(2) 68 L (YR)(H)(T)(KE) 64 W W(25) 0.15 138/0 2.28 18 C (KER)(QHD)(FYMW)(N) F(58) 19 H (E)(QM)(KD)(NLPI) Y(15)Q 62 P (R)(Y)(H)(K) 59 G G(43) 0.16 27/15 2.50 80 V (YR)(KE)(H)(QD) N(54) 11 F (K)(E)(Q)(D) A(1) 64 W (KE)(TD)(Q)(SCRG) 14 N N(80) 0.17 36/19 2.56 59 G (E)(R)(K)(H) Q(6) 14 N (Y)(FW)(H)(E) K(3)GT 53 Q (Y)(H)(FW)(T) H(6)SA 76 V (Y)(R)(KE)(H) 53 Q Q(75) 0.18 47/0 2.64 77 A (KR)(E)(Y)(QH) L(3) 60 A (Y)(R)(H)(KE) I(11) 50 I (R)(Y)(KH)(TE) A(2)E 32 L (Y)(R)(H)(T) V(2) S(1). Table 3. List of disruptive mutations for the top 25% of residues in 76 V V(87) 0.19 86/9 2.28 1a2sA, that are at the interface with heme c. L(4) M(6) A(1) Figure 4 shows residues in 1a2sA colored by their importance, at the 77 A A(84) 0.20 8/3 4.04 interface with 1a2sHEC19. S(10) 2.4.3 Possible novel functional surfaces at 25% coverage. One continued in next column group of residues is conserved on the 1a2sA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1a2s. It is shown in Fig. 5. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. The residues belonging to this surface ”patch” are listed in Table 3 Table 4. continued res type substitutions(%) cvg 79 Y Y(93)F(4)W(1) 0.14 64 W W(25)F(58)Y(15) 0.15 Q 59 G G(43)N(54)A(1) 0.16 14 N N(80)Q(6)K(3)GT 0.17 H(6)SA 53 Q Q(75)L(3)I(11) 0.18 A(2)EV(2)S(1). 22 G G(87).(4)EAN(1) 0.21 D(2)SZ 60 A A(69)G(5)N(8) 0.23 V(10)P(2)SMEK 32 L L(88).V(1)IA 0.25 Q(2)G(1)PDM Table 4. Residues forming surface ”patch” in 1a2sA.
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