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1Dwo Lichtarge Lab 2006 Pages 1–7 1dwo Evolutionary trace report by report maker April 9, 2010 4.3.1 Alistat 6 4.3.2 CE 6 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 1dwo): Title: Crystal structure of hydroxynitrile lyase from manihot esculenta in complex with substrates acetone and chloroace- tone:implications for the mechanism of cyanogenesis Compound: Mol id: 1; molecule: hydroxynitrile lyase; chain: a, b; synonym: (s)-acetone-cyanohydrin lyase, (s)- hydroxynitrilase; ec: 4.2.1.37; engineered: yes; other details: acetone complex Organism, scientific name: Manihot Esculenta; CONTENTS 1dwo contains a single unique chain 1dwoA (262 residues long) and its homologue 1dwoB. 1 Introduction 1 2 Chain 1dwoA 1 2 CHAIN 1DWOA 2.1 P52705 overview 1 2.1 P52705 overview 2.2 Multiple sequence alignment for 1dwoA 1 2.3 Residue ranking in 1dwoA 1 From SwissProt, id P52705, 94% identical to 1dwoA: 2.4 Top ranking residues in 1dwoA and their position on Description: (S)-acetone-cyanohydrin lyase (EC 4.1.2.39) ((S)- the structure 1 hydroxynitrile lyase) ((S)-hydroxynitrilase) (Oxynitrilase). 2.4.1 Clustering of residues at 25% coverage. 2 Organism, scientific name: Manihot esculenta (Cassava) (Manioc). 2.4.2 Overlap with known functional surfaces at Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 25% coverage. 2 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 2.4.3 Possible novel functional surfaces at 25% eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; coverage. 4 Crotonoideae; Manihoteae; Manihot. Function: Involved in cyanogenesis, the release of HCN from inju- 3 Notes on using trace results 5 red tissues. Decomposes a varieties of (R) or (S) cyanohydrins into 3.1 Coverage 5 HCN and the corresponding aldehydes and ketones. The natural 3.2 Known substitutions 5 substrate of this enzyme is (S)-acetone cyanohydrin. 3.3 Surface 5 Catalytic activity: 2-hydroxyisobutyronitrile = cyanide + acetone. 3.4 Number of contacts 6 Subunit: Homotrimer. 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 6 and this statement is not removed. 1 Lichtarge lab 2006 2.4 Top ranking residues in 1dwoA 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 1dwoA 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 -4-127 in 1dwoA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 2. Residues 128-258 in 1dwoA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) 2.2 Multiple sequence alignment for 1dwoA For the chain 1dwoA, the alignment 1dwoA.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 1dwoA.msf. Its statistics, from the alistat program are the following: Fig. 3. Residues in 1dwoA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 33 Total number of residues: 8134 Smallest: 117 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Largest: 262 top 25% of all residues, this time colored according to clusters they Average length: 246.5 belong to. The clusters in Fig.4 are composed of the residues listed Alignment length: 262 in Table 1. Average identity: 43% Table 1. Most related pair: 99% cluster size member Most unrelated pair: 10% color residues Most distant seq: 40% red 62 6,7,8,9,10,11,14,15,16,17,19 26,27,30,31,35,37,40,42,57 Furthermore, <1% of residues show as conserved in this ali- 60,61,76,77,78,79,80,82,83 gnment. 87,89,93,96,101,102,105,107 The alignment consists of 96% eukaryotic ( 96% plantae) 108,162,166,169,173,175,190 sequences. (Descriptions of some sequences were not readily availa- 195,196,197,200,208,216,220 ble.) The file containing the sequence descriptions can be found in 224,228,235,236,239,241,243 the attachment, under the name 1dwoA.descr. 250,253,254,257 Table 1. Clusters of top ranking residues in 1dwoA. 2.3 Residue ranking in 1dwoA The 1dwoA sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues 2.4.2 Overlap with known functional surfaces at 25% coverage. in 1dwoA can be found in the file called 1dwoA.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 Fig. 4. Residues in 1dwoA, 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. Acetone binding site. Table 2 lists the top 25% of residues at the interface with 1dwoSACN259 (acetone). 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 antn (%) bb (A˚ ) 236 H H(96) 0.02 2/0 4.38 site .(3) 11 T G(75) 0.08 9/0 2.90 T(18) .(3) N(3) 80 S S(87) 0.12 9/2 3.01 site A(3) .(6) D(3) 14 H H(84) 0.15 3/0 4.15 I(3) L(6) .(3) F(3) Table 2. The top 25% of residues in 1dwoA at the interface with ace- tone.(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 mutations (%) bb (A˚ ) 236 H (E)(TQMD)(SNVCLAPIG)(K) .(3) 11 T (R)(K)(FWH)(M) V(3) 80 S (R)(K)(H)(FQW) 19 W W(90) 0.06 8/7 3.79 14 H (E)(T)(Q)(D) Y(6) .(3) Table 3. List of disruptive mutations for the top 25% of residues in 42 G G(93) 0.07 3/3 3.90 1dwoA, that are at the interface with acetone. .(6) 16 A A(81) 0.09 13/9 3.19 G(15) .(3) 37 D D(87) 0.14 1/0 4.45 .(6) E(3) N(3) 166 E D(87) 0.14 2/1 4.69 .(3) E(9) 35 A A(84) 0.19 1/0 3.76 V(9) .(6) 173 V L(84) 0.21 21/14 3.62 .(3) V(6) S(6) 27 E R(36) 0.23 3/0 4.02 E(51) .(6) K(3) V(3) Table 4. The top 25% of residues in 1dwoA at the interface with 1dwoB. (Field names: res: residue number in the PDB entry; type: amino acid type; Fig. 5. Residues in 1dwoA, at the interface with acetone, colored by their substs: substitutions seen in the alignment; with the percentage of each type relative importance. The ligand (acetone) is colored green. Atoms further than in the bracket; noc/bb: number of contacts with the ligand, with the number of 30A˚ away from the geometric center of the ligand, as well as on the line of contacts realized through backbone atoms given in the bracket; dist: distance sight to the ligand were removed. (See Appendix for the coloring scheme for of closest apporach to the ligand. ) the protein chain 1dwoA.) Figure 5 shows residues in 1dwoA colored by their importance, at the interface with 1dwoSACN259. Table 5. Interface with 1dwoB.Table 4 lists the top 25% of residues at res type disruptive the interface with 1dwoB. The following table (Table 5) suggests mutations possible disruptive replacements for these residues (see Section 3.6). 17 W (KE)(TQD)(SNCG)(R) 175 R (T)(D)(Y)(VCAG) Table 4. 169 L (Y)(R)(H)(T) res type subst’s cvg noc/ dist 19 W (K)(E)(Q)(D) (%) bb (A˚ ) 42 G (KER)(FQMWHD)(NLPI)(Y) 17 W W(96) 0.01 17/11 3.68 16 A (KER)(Y)(HD)(Q) .(3) 37 D (R)(FWH)(YVCAG)(TK) 175 R R(93) 0.03 10/1 3.88 166 E (FW)(H)(VCAG)(R) .(3) 35 A (YE)(KR)(D)(H) K(3) 173 V (R)(KY)(E)(H) 169 L L(93) 0.05 34/8 3.72 27 E (FW)(YH)(CG)(VA) continued in next column Table 5.
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