Pages 1–8 1a59 Evolutionary trace report by report maker August 8, 2010 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1a59): Title: Cold-active citrate synthase Compound: Mol id: 1; molecule: citrate synthase; chain: a; engineered: yes Organism, scientific name: Antarctic Bacterium Ds2-3r; 1a59 contains a single unique chain 1a59A (377 residues long). 2 CHAIN 1A59A 2.1 O34002 overview From SwissProt, id O34002, 100% identical to 1a59A: CONTENTS Description: Citrate synthase (EC 2.3.3.1). 1 Introduction 1 Organism, scientific name: Antarctic bacterium DS2-3R. Taxonomy: Bacteria. 2 Chain 1a59A 1 Catalytic activity: Acetyl-CoA + H(2)O + oxaloacetate = citrate + 2.1 O34002 overview 1 CoA. 2.2 Multiple sequence alignment for 1a59A 1 Biophysicochemical properties: 2.3 Residue ranking in 1a59A 1 Temperature dependence: Optimum temperature is 31 degrees Cel- 2.4 Top ranking residues in 1a59A and their position on sius. Cold-active. Is rapidly inactivated at 45 degrees Celsius, and the structure 2 shows significant activity at 10 degrees Celsius and below; 2.4.1 Clustering of residues at 25% coverage. 2 Pathway: Tricarboxylic acid cycle. 2.4.2 Overlap with known functional surfaces at Subunit: Homodimer. 25% coverage. 2 Miscellaneous: Citrate synthase is found in nearly all cells capable of oxidative metabolism. 3 Notes on using trace results 6 Similarity: Belongs to the citrate synthase family. 3.1 Coverage 6 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 6 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 6 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 6 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 6 and this statement is not removed. 3.6 Mutation suggestions 6 2.2 Multiple sequence alignment for 1a59A 4 Appendix 7 For the chain 1a59A, the alignment 1a59A.msf (attached) with 120 4.1 File formats 7 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 7 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 7 using Muscle program. It can be found in the attachment to this 4.3.1 Alistat 7 report, under the name of 1a59A.msf. Its statistics, from the alistat 4.3.2 CE 7 program are the following: 1 Lichtarge lab 2006 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 2-189 in 1a59A colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 2. Residues 190-378 in 1a59A colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 3. Residues in 1a59A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 120 Total number of residues: 43727 Smallest: 319 Largest: 377 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Average length: 364.4 top 25% of all residues, this time colored according to clusters they Alignment length: 377 belong to. The clusters in Fig.4 are composed of the residues listed Average identity: 40% in Table 1. Most related pair: 99% Most unrelated pair: 26% Table 1. Most distant seq: 39% cluster size member color residues red 83 8,9,17,19,20,22,23,27,29,31 Furthermore, 3% of residues show as conserved in this alignment. 32,33,47,51,52,55,58,92,93 The alignment consists of 5% eukaryotic ( 3% plantae), 85% 94,180,182,183,185,186,187 prokaryotic, and 10% archaean sequences. (Descriptions of some 189,190,191,192,193,196,200 sequences were not readily available.) The file containing the 201,212,214,216,218,219,220 sequence descriptions can be found in the attachment, under the name 221,222,223,224,225,265,266 1a59A.descr. 267,268,269,270,271,272,276 277,278,279,302,306,315,317 2.3 Residue ranking in 1a59A 318,319,320,321,322,323,324 The 1a59A sequence is shown in Figs. 1–2, with each residue colored 327,337,338,341,342,345,348 according to its estimated importance. The full listing of residues 349,351,352,355,356,362,364 in 1a59A can be found in the file called 1a59A.ranks sorted in the 365 attachment. blue 5 149,158,159,160,162 yellow 2 369,371 2.4 Top ranking residues in 1a59A and their position on the structure Table 1. Clusters of top ranking residues in 1a59A. In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1a59A colored 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) S(3) R(1) 220 L L(59) 0.18 27/16 2.91 S(2) K(14) A(23) 265 M M(76) 0.23 27/10 3.13 I(13) S(5) A(1)FW P(1) Table 2. The top 25% of residues in 1a59A at the interface with coenzyme a.(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. ) Fig. 4. Residues in 1a59A, colored according to the cluster they belong to: Table 3. red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The res type disruptive corresponding Pymol script is attached. mutations 221 H (E)(TQMD)(SNKVCLAPIG)(YR) 224 A (KYER)(QHD)(N)(FTMW) 2.4.2 Overlap with known functional surfaces at 25% coverage. 266 G (KER)(FQMWHD)(NYLPI)(SVA) The name of the ligand is composed of the source PDB identifier 269 H (E)(TQMD)(SNKVCLAPIG)(YR) and the heteroatom name used in that file. 318 N (Y)(FTWH)(SEVCARG)(MD) Coenzyme a binding site. Table 2 lists the top 25% of residues at 320 D (R)(FWH)(YVCAG)(K) the interface with 1a59COA380 (coenzyme a). The following table 268 G (KER)(QHD)(FYMW)(N) (Table 3) suggests possible disruptive replacements for these residues 267 F (KE)(T)(R)(D) (see Section 3.6). 270 R (TYD)(E)(SCG)(FVLAWPI) 315 I (Y)(R)(TH)(CG) Table 2. 219 P (Y)(R)(H)(TE) res type subst’s cvg noc/ dist 220 L (Y)(R)(H)(T) ˚ (%) bb (A) 265 M (Y)(TR)(H)(CG) 221 H H(100) 0.03 9/9 3.79 224 A A(100) 0.03 8/3 3.43 Table 3. List of disruptive mutations for the top 25% of residues in 266 G G(100) 0.03 8/8 2.83 1a59A, that are at the interface with coenzyme a. 269 H H(100) 0.03 19/19 3.54 318 N N(100) 0.03 10/0 3.08 320 D D(95) 0.04 3/0 4.19 Figure 5 shows residues in 1a59A colored by their importance, at the E(4) interface with 1a59COA380. 268 G G(99)V 0.05 24/24 3.25 Citric acid binding site. Table 4 lists the top 25% of residues at the 267 F F(96)IL 0.08 28/26 2.80 interface with 1a59CIT379 (citric acid). The following table (Table VM 5) suggests possible disruptive replacements for these residues (see 270 R R(80) 0.09 25/8 3.07 Section 3.6). P(13) Table 4. A(6) res type subst’s cvg noc/ dist 315 I I(25) 0.11 18/0 3.51 (%) bb (A˚ ) L(61) 186 H H(99)Q 0.03 34/5 2.75 M(13) 221 H H(100) 0.03 39/11 2.81 219 P AP(94) 0.15 8/8 3.51 222 G G(100) 0.03 9/9 3.78 continued in next column 269 H H(100) 0.03 24/0 2.89 continued in next column 3 Table 5. res type disruptive mutations 186 H (TE)(D)(SVMCAG)(QLPI) 221 H (E)(TQMD)(SNKVCLAPIG)(YR) 222 G (KER)(FQMWHD)(NYLPI)(SVA) 269 H (E)(TQMD)(SNKVCLAPIG)(YR) 278 R (TD)(SYEVCLAPIG)(FMW)(N) 320 D (R)(FWH)(YVCAG)(K) 189 N (Y)(H)(FW)(R) 341 F (KE)(TQD)(SNCG)(R) 345 R (TD)(SVCLAPIG)(YE)(FMW) 190 A (YE)(R)(K)(H) 270 R (TYD)(E)(SCG)(FVLAWPI) 220 L (Y)(R)(H)(T) Table 5. List of disruptive mutations for the top 25% of residues in 1a59A, that are at the interface with citric acid. Fig. 5. Residues in 1a59A, at the interface with coenzyme a, colored by their relative importance. The ligand (coenzyme a) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1a59A.) Table 4.