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1E6v Lichtarge Lab 2006 Pages 1–18 1e6v Evolutionary trace report by report maker July 11, 2009 4.4.1 Clustering of residues at 25% coverage. 9 4.4.2 Overlap with known functional surfaces at 25% coverage. 10 4.4.3 Possible novel functional surfaces at 25% coverage. 15 5 Notes on using trace results 16 5.1 Coverage 16 5.2 Known substitutions 16 5.3 Surface 16 5.4 Number of contacts 16 5.5 Annotation 16 5.6 Mutation suggestions 16 6 Appendix 16 6.1 File formats 16 6.2 Color schemes used 16 6.3 Credits 17 6.3.1 Alistat 17 6.3.2 CE 17 6.3.3 DSSP 17 6.3.4 HSSP 17 CONTENTS 6.3.5 LaTex 17 6.3.6 Muscle 17 1 Introduction 1 6.3.7 Pymol 17 6.4 Note about ET Viewer 17 2 Chain 1e6vC 1 6.5 Citing this work 17 2.1 Q49604 overview 1 6.6 About report maker 17 2.2 Multiple sequence alignment for 1e6vC 1 6.7 Attachments 17 2.3 Residue ranking in 1e6vC 1 2.4 Top ranking residues in 1e6vC and their position on 1 INTRODUCTION the structure 2 2.4.1 Clustering of residues at 25% coverage. 2 From the original Protein Data Bank entry (PDB id 1e6v): 2.4.2 Overlap with known functional surfaces at Title: Methyl-coenzyme m reductase from methanopyrus kandleri 25% coverage. 2 Compound: Mol id: 1; molecule: methyl-coenzyme m reductase i alpha subunit; chain: a, d; mol id: 2; molecule: methyl-coenzyme m 3 Chain 1e6vA 6 reductase i beta subunit; chain: b, e; mol id: 3; molecule: methyl- 3.1 Q49605 overview 6 coenzyme m reductase i gamma subunit; chain: c, f 3.2 Multiple sequence alignment for 1e6vA 7 Organism, scientific name: Methanopyrus Kandleri; 3.3 Residue ranking in 1e6vA 7 1e6v contains unique chains 1e6vC (248 residues), 1e6vA (545 3.4 Top ranking residues in 1e6vA and their position on residues), and 1e6vB (436 residues) 1e6vF is a homologue of chain the structure 7 1e6vC. 1e6vD is a homologue of chain 1e6vA. 1e6vE is a homologue 3.4.1 Clustering of residues at 32% coverage. 7 of chain 1e6vB. 4 Chain 1e6vB 8 2 CHAIN 1E6VC 4.1 Q49601 overview 8 4.2 Multiple sequence alignment for 1e6vB 8 2.1 Q49604 overview 4.3 Residue ranking in 1e6vB 8 From SwissProt, id Q49604, 93% identical to 1e6vC: 4.4 Top ranking residues in 1e6vB and their position on Description: Methyl coenzyme M reductase, gamma subunit. the structure 8 Organism, scientific name: Methanopyrus kandleri. 1 Lichtarge lab 2006 2.4 Top ranking residues in 1e6vC and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1e6vC colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 1. Residues 7-130 in 1e6vC colored by their relative importance. (See Appendix, Fig.26, for the coloring scheme.) Fig. 2. Residues 131-254 in 1e6vC colored by their relative importance. (See Appendix, Fig.26, for the coloring scheme.) Taxonomy: Archaea; Euryarchaeota; Methanopyri; Methanopyrales; Methanopyraceae; Methanopyrus. 2.2 Multiple sequence alignment for 1e6vC For the chain 1e6vC, the alignment 1e6vC.msf (attached) with 44 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 1e6vC.msf. Its statistics, from the Fig. 3. Residues in 1e6vC, colored by their relative importance. Clockwise: alistat program are the following: front, back, top and bottom views. Format: MSF Number of sequences: 44 Total number of residues: 10782 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 238 top 25% of all residues, this time colored according to clusters they Largest: 248 belong to. The clusters in Fig.4 are composed of the residues listed Average length: 245.0 in Table 1. Alignment length: 248 Average identity: 59% Table 1. Most related pair: 99% cluster size member Most unrelated pair: 46% color residues Most distant seq: 65% red 51 31,33,41,46,47,49,50,53,57 58,59,60,62,79,80,83,85,87 Furthermore, 17% of residues show as conserved in this alignment. 88,90,93,94,102,103,105,115 The alignment consists of 13% prokaryotic, and 56% archaean 117,119,121,122,123,124,128 sequences. (Descriptions of some sequences were not readily availa- 130,131,135,150,155,156,159 ble.) The file containing the sequence descriptions can be found in 160,161,162,165,166,170,172 the attachment, under the name 1e6vC.descr. 178,192,206,208 blue 3 11,19,20 2.3 Residue ranking in 1e6vC yellow 3 99,214,218 The 1e6vC sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues Table 1. Clusters of top ranking residues in 1e6vC. in 1e6vC can be found in the file called 1e6vC.ranks sorted in the attachment. 2 Fig. 4. Residues in 1e6vC, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. 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. Factor 430 binding site. Table 2 lists the top 25% of residues at the interface with 1e6vDF43553 (factor 430). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 5.6). Table 2. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 122 S S(100) 0.18 16/10 2.92 site 123 G G(100) 0.18 12/12 2.41 site 156 G G(100) 0.18 2/2 4.64 159 V V(100) 0.18 22/10 2.77 161 G G(100) 0.18 4/4 3.82 162 H H(100) 0.18 8/1 3.26 121 L L(97) 0.23 13/6 4.01 site S(2) 124 R R(97) 0.23 23/1 3.60 site G(2) 160 H H(97) 0.23 25/11 2.68 site Y(2) Table 2. The top 25% of residues in 1e6vC at the interface with factor 430.(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 num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 3 Table 3. Table 4. continued res type disruptive res type subst’s cvg noc/ dist antn mutations (%) bb (A˚ ) 122 S (KR)(FQMWH)(NYELPI)(D) 90 Q Q(100) 0.18 1/0 4.35 123 G (KER)(FQMWHD)(NYLPI)(SVA) 117 D D(100) 0.18 1/0 4.70 156 G (KER)(FQMWHD)(NYLPI)(SVA) 128 E E(100) 0.18 21/0 3.00 159 V (KYER)(QHD)(N)(FTMW) 156 G G(100) 0.18 18/18 3.00 161 G (KER)(FQMWHD)(NYLPI)(SVA) 88 Y Y(97) 0.23 37/2 3.32 162 H (E)(TQMD)(SNKVCLAPIG)(YR) S(2) 121 L (R)(Y)(H)(K) 124 R R(97) 0.23 20/0 2.77 site 124 R (D)(E)(TYLPI)(SFVMAW) G(2) 160 H (E)(QM)(KD)(TNVLAPI) 160 H H(97) 0.23 27/0 3.77 site Y(2) Table 3. List of disruptive mutations for the top 25% of residues in 45 G A(20) 0.25 1/1 4.35 1e6vC, that are at the interface with factor 430. G(77) S(2) Table 4. The top 25% of residues in 1e6vC at the interface with 1e6vD. (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 contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 5. res type disruptive mutations 85 R (TD)(SYEVCLAPIG)(FMW)(N) 87 R (TD)(SYEVCLAPIG)(FMW)(N) 90 Q (Y)(FTWH)(SVCAG)(D) 117 D (R)(FWH)(KYVCAG)(TQM) 128 E (FWH)(YVCARG)(T)(SNKLPI) 156 G (KER)(FQMWHD)(NYLPI)(SVA) 88 Y (K)(QM)(R)(NELPI) 124 R (D)(E)(TYLPI)(SFVMAW) 160 H (E)(QM)(KD)(TNVLAPI) 45 G (KR)(E)(QH)(FMW) Table 5. List of disruptive mutations for the top 25% of residues in Fig. 5. Residues in 1e6vC, at the interface with factor 430, colored by their 1e6vC, that are at the interface with 1e6vD. relative importance. The ligand (factor 430) is colored green. Atoms further A than 30 ˚ away from the geometric center of the ligand, as well as on the line Figure 6 shows residues in 1e6vC colored by their importance, at the of sight to the ligand were removed. (See Appendix for the coloring scheme interface with 1e6vD. for the protein chain 1e6vC.) Interface with 1e6vB.Table 6 lists the top 25% of residues at the interface with 1e6vB.
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