Pages 1–7 1qj4 Evolutionary trace report by report maker January 28, 2010 4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 7 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 1qj4): Title: Hydroxynitrile-lyase from hevea brasiliensis at atomic resolu- tion Compound: Mol id: 1; molecule: hydroxynitrile lyase; chain: a; synonym: oxynitrile lyase; ec: 4.2.1.39; engineered: yes Organism, scientific name: Hevea Brasiliensis; 1qj4 contains a single unique chain 1qj4A (256 residues long). CONTENTS 1 Introduction 1 2 CHAIN 1QJ4A 2 Chain 1qj4A 1 2.1 P52704 overview 2.1 P52704 overview 1 2.2 Multiple sequence alignment for 1qj4A 1 From SwissProt, id P52704, 100% identical to 1qj4A: 2.3 Residue ranking in 1qj4A 1 Description: (S)-acetone-cyanohydrin lyase (EC 4.1.2.39) ((S)- 2.4 Top ranking residues in 1qj4A and their position on hydroxynitrile lyase) ((S)-hydroxynitrilase) (Oxynitrilase). the structure 2 Organism, scientific name: Hevea brasiliensis (Para rubber tree). 2.4.1 Clustering of residues at 25% coverage. 2 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4.2 Overlap with known functional surfaces at Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 25% coverage. 2 eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; 2.4.3 Possible novel functional surfaces at 25% Crotonoideae; Micrandreae; Hevea. coverage. 4 Function: Involved in cyanogenesis, the release of HCN from inju- red tissues. Decomposes a varieties of (R) or (S) cyanohydrins into 3 Notes on using trace results 5 HCN and the corresponding aldehydes and ketones. The natural 3.1 Coverage 5 substrate of this enzyme is (S)-acetone cyanohydrin. 3.2 Known substitutions 6 Catalytic activity: 2-hydroxyisobutyronitrile = cyanide + acetone. 3.3 Surface 6 Subunit: Homodimer. 3.4 Number of contacts 6 Ptm: The N-terminus is blocked. 3.5 Annotation 6 Similarity: Belongs to the AB hydrolase superfamily. Hydroxynitrile 3.6 Mutation suggestions 6 lyase family. About: This Swiss-Prot entry is copyright. It is produced through a 4 Appendix 6 collaboration between the Swiss Institute of Bioinformatics and the 4.1 File formats 6 EMBL outstation - the European Bioinformatics Institute. There are 4.2 Color schemes used 6 no restrictions on its use as long as its content is in no way modified 4.3 Credits 7 and this statement is not removed. 1 Lichtarge lab 2006 2.4 Top ranking residues in 1qj4A 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 1qj4A 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 2-129 in 1qj4A colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 2. Residues 130-257 in 1qj4A colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) 2.2 Multiple sequence alignment for 1qj4A For the chain 1qj4A, the alignment 1qj4A.msf (attached) with 33 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 1qj4A.msf. Its statistics, from the Fig. 3. Residues in 1qj4A, colored by their relative importance. Clockwise: alistat program are the following: front, back, top and bottom views. Format: MSF Number of sequences: 33 Total number of residues: 8290 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 237 top 25% of all residues, this time colored according to clusters they Largest: 256 belong to. The clusters in Fig.4 are composed of the residues listed Average length: 251.2 in Table 1. Alignment length: 256 Table 1. Average identity: 42% cluster size member Most related pair: 99% color residues Most unrelated pair: 26% red 63 7,8,9,10,11,14,15,16,17,19 Most distant seq: 35% 21,23,26,27,30,31,33,35,37 38,40,42,57,60,61,72,73,76 Furthermore, 3% of residues show as conserved in this alignment. 77,78,79,80,82,83,87,89,94 The alignment consists of 93% eukaryotic ( 93% plantae), and 3% 96,101,102,105,107,108,161 prokaryotic sequences. (Descriptions of some sequences were not 164,165,168,172,174,194,195 readily available.) The file containing the sequence descriptions can 196,199,207,215,234,235,238 be found in the attachment, under the name 1qj4A.descr. 240,242,245,249,252 Table 1. Clusters of top ranking residues in 1qj4A. 2.3 Residue ranking in 1qj4A The 1qj4A sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues 2.4.2 Overlap with known functional surfaces at 25% coverage. in 1qj4A can be found in the file called 1qj4A.ranks sorted in the The name of the ligand is composed of the source PDB identifier attachment. and the heteroatom name used in that file. 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) K(3) V(3) 172 L L(81) 0.19 19/6 3.74 V(6) S(12) 21 K K(87) 0.20 6/3 4.04 R(12) 23 K A(21) 0.21 25/1 2.77 V(18) K(51) I(9) 164 E E(72) 0.25 33/19 3.13 G(6) K(9) Q(12) Table 2. The top 25% of residues in 1qj4A at the interface with 1qj4A1. (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 Fig. 4. Residues in 1qj4A, colored according to the cluster they belong to: in the bracket; noc/bb: number of contacts with the ligand, with the number of red, followed by blue and yellow are the largest clusters (see Appendix for contacts realized through backbone atoms given in the bracket; dist: distance the coloring scheme). Clockwise: front, back, top and bottom views. The of closest apporach to the ligand. ) corresponding Pymol script is attached. Table 3. Interface with 1qj4A1.Table 2 lists the top 25% of residues at res type disruptive the interface with 1qj4A1. The following table (Table 3) suggests mutations possible disruptive replacements for these residues (see Section 3.6). 17 W (KE)(TQD)(SNCRG)(M) 42 G (KER)(FQMWHD)(NYLPI)(SVA) Table 2. 168 L (YR)(H)(TKE)(SQCDG) res type subst’s cvg noc/ dist 174 R (D)(TY)(FEVLAWPI)(CG) ˚ (%) bb (A) 37 D (R)(FWH)(Y)(VCAG) 17 W W(100) 0.03 21/14 3.69 16 A (KER)(Y)(QHD)(N) 42 G G(100) 0.03 4/4 3.74 19 W (K)(E)(Q)(D) 168 L L(96) 0.06 33/2 3.55 165 E (FWH)(R)(YVCAG)(T) V(3) 35 A (KR)(YE)(H)(Q) 174 R T(3) 0.06 7/0 3.96 27 E (FYW)(H)(CG)(TVA) R(93) 172 L (R)(Y)(H)(K) K(3) 21 K (Y)(T)(FW)(SVCAG) 37 D D(93) 0.08 1/0 4.96 23 K (Y)(T)(FW)(H) E(3) 164 E (FW)(H)(Y)(VA) N(3) 16 A A(84) 0.09 11/8 3.32 Table 3. List of disruptive mutations for the top 25% of residues in 1qj4A, G(15) that are at the interface with 1qj4A1. 19 W W(93) 0.10 6/5 3.94 Y(6) 165 E D(90) 0.11 1/1 4.92 Figure 5 shows residues in 1qj4A colored by their importance, at the E(9) interface with 1qj4A1. 35 A S(3) 0.12 1/0 3.95 Glycerol binding site. Table 4 lists the top 25% of residues at the A(87) interface with 1qj4GOL300 (glycerol). The following table (Table V(9) 5) suggests possible disruptive replacements for these residues (see 27 E E(60) 0.18 4/0 4.14 Section 3.6). R(33) continued in next column 3 Table 5. continued res type disruptive mutations 14 H (E)(T)(Q)(D) Table 5. List of disruptive mutations for the top 25% of residues in 1qj4A, that are at the interface with glycerol. Fig. 5. Residues in 1qj4A, at the interface with 1qj4A1, colored by their rela- tive importance. 1qj4A1 is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 1qj4A.) Table 4. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 235 H H(100) 0.03 16/0 3.05 site 80 S S(90) 0.12 34/4 2.52 site A(3) Fig. 6. Residues in 1qj4A, at the interface with glycerol, colored by their D(6) relative importance. The ligand (glycerol) is colored green. Atoms further 11 T G(81) 0.13 25/2 2.28 than 30A˚ away from the geometric center of the ligand, as well as on the line T(15) of sight to the ligand were removed. (See Appendix for the coloring scheme N(3) for the protein chain 1qj4A.) 14 H S(3) 0.22 3/0 4.15 H(78) I(3) Figure 6 shows residues in 1qj4A colored by their importance, at the F(9) interface with 1qj4GOL300.