Pages 1–7 1cts Evolutionary trace report by report maker July 3, 2009 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 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 1cts): Title: Crystallographic refinement and atomic models of two diffe- rent forms of citrate synthase at 2.7 and 1.7 angstroms resolution Compound: Mol id: 1; molecule: citrate synthase; chain: a; ec: 4.1.3.7; engineered: yes Organism, scientific name: Sus Scrofa 1cts contains a single unique chain 1ctsA (437 residues long). 2 CHAIN 1CTSA 2.1 P00889 overview CONTENTS From SwissProt, id P00889, 100% identical to 1ctsA: 1 Introduction 1 Description: Citrate synthase, mitochondrial precursor (EC 2.3.3.1). Organism, scientific name: Sus scrofa (Pig). 2 Chain 1ctsA 1 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 2.1 P00889 overview 1 Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; 2.2 Multiple sequence alignment for 1ctsA 1 Suina; Suidae; Sus. 2.3 Residue ranking in 1ctsA 1 Catalytic activity: Acetyl-CoA + H(2)O + oxaloacetate = citrate + 2.4 Top ranking residues in 1ctsA and their position on CoA. the structure 1 Pathway: Tricarboxylic acid cycle. 2.4.1 Clustering of residues at 25% coverage. 1 Subunit: Homodimer. 2.4.2 Overlap with known functional surfaces at Subcellular location: Mitochondrial matrix. 25% coverage. 2 Miscellaneous: Citrate synthase is found in nearly all cells capable of oxidative metabolism. 3 Notes on using trace results 5 Similarity: Belongs to the citrate synthase family. 3.1 Coverage 5 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 5 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 5 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 5 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 5 and this statement is not removed. 3.6 Mutation suggestions 5 2.2 Multiple sequence alignment for 1ctsA 4 Appendix 6 For the chain 1ctsA, the alignment 1ctsA.msf (attached) with 193 4.1 File formats 6 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 6 database, and fragments shorter than 75% of the query as well as 4.3 Credits 6 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 6 to this report, under the name of 1ctsA.msf. Its statistics, from the 4.3.2 CE 6 alistat program are the following: 1 Lichtarge lab 2006 2.4 Top ranking residues in 1ctsA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 3 shows residues in 1ctsA 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. Fig. 1. Residues 1-218 in 1ctsA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 2. Residues 219-437 in 1ctsA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 3. Residues in 1ctsA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 193 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 80831 top 25% of all residues, this time colored according to clusters they Smallest: 329 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 437 in Table 1. Average length: 418.8 Table 1. Alignment length: 437 Average identity: 48% cluster size member Most related pair: 99% color residues Most unrelated pair: 22% red 98 56,58,59,63,64,66,71,89,90 Most distant seq: 38% 94,96,132,136,137,138,140 152,154,174,178,180,189,229 231,235,237,238,239,240,241 Furthermore, 1% of residues show as conserved in this alignment. 242,243,244,245,246,249,250 The alignment consists of 30% eukaryotic ( 2% vertebrata, 1% 251,252,253,254,255,256,257 arthropoda, 15% fungi, 5% plantae), and 7% prokaryotic sequences. 260,264,265,268,269,270,271 (Descriptions of some sequences were not readily available.) The file 272,273,274,275,276,277,278 containing the sequence descriptions can be found in the attachment, 279,281,282,284,314,316,317 under the name 1ctsA.descr. 318,319,320,321,322,323,324 327,328,329,330,370,372,373 2.3 Residue ranking in 1ctsA 374,375,378,379,382,386,393 394,395,397,398,400,401,404 The 1ctsA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues continued in next column in 1ctsA can be found in the file called 1ctsA.ranks sorted in the attachment. 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) Table 2. The top 25% of residues in 1ctsA at the interface with citric acid.(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. ) Table 3. res type disruptive mutations 238 H (E)(TQMD)(SNKVCLAPIG)(YR) 274 H (TEQM)(KVCAG)(SNLPDI)(R) 242 N (Y)(FWH)(TER)(SVA) 273 L (T)(Y)(ER)(CG) 329 R (TD)(SVCLAPIG)(YE)(FMW) 397 F (K)(E)(Q)(D) 401 R (T)(D)(CG)(Y) Fig. 4. Residues in 1ctsA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for Table 3. List of disruptive mutations for the top 25% of residues in 1ctsA, the coloring scheme). Clockwise: front, back, top and bottom views. The that are at the interface with citric acid. corresponding Pymol script is attached. Table 1. continued cluster size member color residues 420,421,422,423,424 blue 3 78,79,102 Table 1. Clusters of top ranking residues in 1ctsA. 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. Citric acid binding site. Table 2 lists the top 25% of residues at the interface with 1ctsCIT1 (citric acid). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 238 H H(100) 0.01 37/5 2.62 274 H H(99)D 0.02 29/6 3.26 242 N N(98).C 0.03 25/4 3.36 273 L L(98)RF 0.03 3/3 4.08 Fig. 5. Residues in 1ctsA, at the interface with citric acid, colored by their 329 R R(99). 0.04 2/0 4.49 relative importance. The ligand (citric acid) is colored green. Atoms further 397 F F(98) 0.09 5/0 4.59 than 30A˚ away from the geometric center of the ligand, as well as on the line .(1)Y of sight to the ligand were removed. (See Appendix for the coloring scheme 401 R R(98) 0.09 14/0 2.69 for the protein chain 1ctsA.) .(1)M continued in next column Figure 5 shows residues in 1ctsA colored by their importance, at the interface with 1ctsCIT1. 3 Interface with 1ctsA1.Table 4 lists the top 25% of residues at Table 4. continued the interface with 1ctsA1. The following table (Table 5) suggests res type subst’s cvg noc/ dist possible disruptive replacements for these residues (see Section 3.6). (%) bb (A˚ ) .(2)RAT Table 4. 254 A S(3) 0.15 52/38 2.92 res type subst’s cvg noc/ dist A(83) (%) bb (A˚ ) T(11) 271 G G(100) 0.01 22/22 3.01 G(1)P 274 H H(99)D 0.02 3/2 4.30 255 L N(1) 0.16 38/20 3.15 242 N N(98).C 0.03 2/2 4.97 L(93) 273 L L(98)RF 0.03 53/12 3.15 Q(3)DRV 138 M M(99)V 0.04 1/1 4.52 H 272 P P(98)RE 0.04 48/11 2.92 264 A A(90) 0.17 20/13 3.77 246 H S(5) 0.06 38/3 3.31 G(5) H(86)L S(4) F(7)A 44 G G(90) 0.18 39/39 2.85 268 G A(17) 0.06 17/17 3.48 .(8) G(82)T N(1) 239 E E(97)G. 0.07 24/4 2.58 270 A FA(82) 0.19 4/3 4.09 T(1)D K(6) 241 G Q(5) 0.08 25/25 3.13 S(4) G(86)P W(4) L(6)IFN Y(1) 243 V C(5) 0.08 22/3 3.30 260 L A(4) 0.20 36/13 2.91 V(82) L(75) A(11)LS S(7) 136 H H(97).S 0.09 1/0 4.71 Y(8) DI T(1) 253 S S(93) 0.09 5/4 3.78 F(1)IG A(5) 256 S A(10) 0.21 24/8 2.82 T(1) S(83) 240 G .(11) 0.10 7/7 3.26 G(3)ETV G(76)V .