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1Aj8 Lichtarge Lab 2006 Pages 1–11 1aj8 Evolutionary trace report by report maker November 10, 2009 4.3.3 DSSP 10 4.3.4 HSSP 10 4.3.5 LaTex 10 4.3.6 Muscle 10 4.3.7 Pymol 10 4.4 Note about ET Viewer 10 4.5 Citing this work 10 4.6 About report maker 10 4.7 Attachments 10 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1aj8): Title: Citrate synthase from pyrococcus furiosus Compound: Mol id: 1; molecule: citrate synthase; chain: a, b; ec: 4.1.3.7; engineered: yes Organism, scientific name: Pyrococcus Furiosus; 1aj8 contains a single unique chain 1aj8A (371 residues long) and its homologue 1aj8B. CONTENTS 2 CHAIN 1AJ8A 1 Introduction 1 2.1 Q53554 overview 2 Chain 1aj8A 1 From SwissProt, id Q53554, 100% identical to 1aj8A: 2.1 Q53554 overview 1 Description: Citrate synthase (EC 2.3.3.1). 2.2 Multiple sequence alignment for 1aj8A 1 Organism, scientific name: Pyrococcus furiosus. 2.3 Residue ranking in 1aj8A 1 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 2.4 Top ranking residues in 1aj8A and their position on les; Thermococcaceae; Pyrococcus. the structure 2 Catalytic activity: Acetyl-CoA + H(2)O + oxaloacetate = citrate + 2.4.1 Clustering of residues at 25% coverage. 2 CoA. 2.4.2 Overlap with known functional surfaces at Pathway: Tricarboxylic acid cycle. 25% coverage. 2 Subunit: Homodimer. Similarity: Belongs to the citrate synthase family. 3 Notes on using trace results 9 About: This Swiss-Prot entry is copyright. It is produced through a 3.1 Coverage 9 collaboration between the Swiss Institute of Bioinformatics and the 3.2 Known substitutions 9 EMBL outstation - the European Bioinformatics Institute. There are 3.3 Surface 9 no restrictions on its use as long as its content is in no way modified 3.4 Number of contacts 9 and this statement is not removed. 3.5 Annotation 9 3.6 Mutation suggestions 9 2.2 Multiple sequence alignment for 1aj8A 4 Appendix 9 For the chain 1aj8A, the alignment 1aj8A.msf (attached) with 309 4.1 File formats 9 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 9 database, and fragments shorter than 75% of the query as well as 4.3 Credits 9 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 9 to this report, under the name of 1aj8A.msf. Its statistics, from the 4.3.2 CE 10 alistat program are the following: 1 Lichtarge lab 2006 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 6-190 in 1aj8A colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 2. Residues 191-376 in 1aj8A colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 3. Residues in 1aj8A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 309 Total number of residues: 104073 Smallest: 174 Largest: 371 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Average length: 336.8 top 25% of all residues, this time colored according to clusters they Alignment length: 371 belong to. The clusters in Fig.4 are composed of the residues listed Average identity: 42% in Table 1. Most related pair: 99% Most unrelated pair: 11% Table 1. Most distant seq: 35% cluster size member color residues red 78 9,18,23,30,32,34,52,53,93,94 Furthermore, <1% of residues show as conserved in this ali- 95,177,179,181,182,184,185 gnment. 186,187,188,189,190,191,192 The alignment consists of 4% eukaryotic ( <1% arthropoda, 193,194,195,197,198,199,202 1% plantae), 89% prokaryotic, and 6% archaean sequences. (Des- 203,214,217,218,219,220,221 criptions of some sequences were not readily available.) The file 222,223,224,225,226,227,228 containing the sequence descriptions can be found in the attachment, 230,258,259,260,261,262,263 under the name 1aj8A.descr. 264,265,269,270,271,272,295 305,307,309,310,311,312,313 2.3 Residue ranking in 1aj8A 314,315,316,319,329,330,333 The 1aj8A sequence is shown in Figs. 1–2, with each residue colored 337,340,341,344,347 according to its estimated importance. The full listing of residues blue 8 130,133,137,151,160,161,162 in 1aj8A can be found in the file called 1aj8A.ranks sorted in the 164 attachment. yellow 3 206,208,209 green 2 356,357 2.4 Top ranking residues in 1aj8A and their position on the structure Table 1. Clusters of top ranking residues in 1aj8A. In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 3 shows residues in 1aj8A colored by their 2 Table 2. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 269 D D(93) 0.05 1/0 4.84 .(5)GS 312 D D(90) 0.05 8/0 3.38 site .(5) E(3) 337 R R(78) 0.09 10/0 2.80 .(21)K 263 R R(80) 0.10 2/1 4.64 .(5) A(7) P(6)K 333 F F(78) 0.12 13/0 3.79 .(19)LS TQ 311 V V(71) 0.15 6/0 3.80 .(5) L(12)P I(4) T(2) Fig. 4. Residues in 1aj8A, colored according to the cluster they belong to: A(3) red, followed by blue and yellow are the largest clusters (see Appendix for 222 I S(1) 0.21 2/2 4.22 the coloring scheme). Clockwise: front, back, top and bottom views. The A(41) corresponding Pymol script is attached. .(5) L(41)V K(6)IT 2.4.2 Overlap with known functional surfaces at 25% coverage. R(1) The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Table 2. The top 25% of residues in 1aj8A at the interface with citric Citric acid binding site. Table 2 lists the top 25% of residues at the acid.(Field names: res: residue number in the PDB entry; type: amino acid interface with 1aj8CIT1000 (citric acid). The following table (Table type; substs: substitutions seen in the alignment; with the percentage of each 3) suggests possible disruptive replacements for these residues (see type in the bracket; noc/bb: number of contacts with the ligand, with the num- Section 3.6). ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 2. res type subst’s cvg noc/ dist antn ˚ (%) bb (A) Table 3. 188 H H(99)Q 0.00 32/2 2.81 res type disruptive 191 N N(93) 0.01 28/6 3.14 mutations P(5)T 188 H (TE)(D)(SVMCAG)(QLPI) 271 R R(94) 0.02 19/0 2.75 191 N (Y)(H)(FW)(R) .(5) 271 R (TD)(SVCLAPIG)(YE)(FMW) 224 G G(94) 0.03 4/4 3.59 224 G (R)(KE)(H)(FWD) .(5)P 262 H (E)(T)(D)(M) 262 H H(93) 0.03 30/0 2.96 site 223 H (T)(EQ)(CG)(VA) .(5)N 310 N (Y)(FWH)(TR)(EVCAG) 223 H H(93) 0.04 31/9 2.98 site 192 A (YER)(K)(H)(D) .(5)DIE 269 D (R)(FWH)(K)(Y) 310 N N(94) 0.04 4/0 4.15 312 D (R)(FW)(H)(VCAG) .(5)S 337 R (T)(D)(Y)(VCAG) 192 A A(83) 0.05 1/1 4.98 263 R (T)(YD)(SE)(CG) C(10) 333 F (K)(E)(D)(QR) V(1) 311 V (R)(Y)(K)(E) N(4) 222 I (Y)(R)(H)(T) continued in next column continued in next column 3 Table 3. continued Table 4. continued res type disruptive res type subst’s cvg noc/ dist antn mutations (%) bb (A˚ ) .(5)SMF Table 3. List of disruptive mutations for the top 25% of residues in 1aj8A, R that are at the interface with citric acid. 310 N N(94) 0.04 14/0 3.04 .(5)S 312 D D(90) 0.05 1/0 4.02 site .(5) E(3) 261 G G(93) 0.06 26/26 3.37 .(5)VDS 260 A F(88) 0.10 30/28 2.84 .(5)YA I(1)M V(1)L 263 R R(80) 0.10 30/11 2.65 .(5) A(7) P(6)K 307 I L(73) 0.11 28/0 3.37 .(5) P(1) M(5) I(12)V 221 P P(90) 0.13 4/4 4.22 .(1) S(1) H(1)AVR NKD 258 M M(78) 0.14 19/10 3.62 Fig. 5. Residues in 1aj8A, at the interface with citric acid, colored by their .(5) relative importance. The ligand (citric acid) is colored green. Atoms further S(2)A A˚ than 30 away from the geometric center of the ligand, as well as on the line P(2) of sight to the ligand were removed. (See Appendix for the coloring scheme I(7) for the protein chain 1aj8A.) Y(1)FWN 222 I S(1) 0.21 34/20 2.96 Figure 5 shows residues in 1aj8A colored by their importance, at the A(41) interface with 1aj8CIT1000.
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