Pages 1–8 1hvq Evolutionary trace report by report maker May 22, 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 1hvq): Title: Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor Compound: Mol id: 1; molecule: hevamine a; chain: a; ec: 3.2.1.14, 3.2.1.17; other details: plant endochitinase/lysozyme Organism, scientific name: Hevea Brasiliensis; 1hvq contains a single unique chain 1hvqA (273 residues long). CONTENTS 2 CHAIN 1HVQA 2.1 P23472 overview 1 Introduction 1 From SwissProt, id P23472, 95% identical to 1hvqA: 2 Chain 1hvqA 1 Description: Hevamine A precursor [Includes: Chitinase (EC 2.1 P23472 overview 1 3.2.1.14); Lysozyme (EC 3.2.1.17)]. 2.2 Multiple sequence alignment for 1hvqA 1 Organism, scientific name: Hevea brasiliensis (Para rubber tree). 2.3 Residue ranking in 1hvqA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 1hvqA and their position on Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core the structure 2 eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; 2.4.1 Clustering of residues at 25% coverage. 2 Crotonoideae; Micrandreae; Hevea. 2.4.2 Overlap with known functional surfaces at Function: Bifunctional enzyme with lysozyme / chitinase activity. 25% coverage. 2 May have a role in plugging the latex vessel and cessation of latex 2.4.3 Possible novel functional surfaces at 25% flow. coverage. 4 Catalytic activity: Random hydrolysis of N-acetyl-beta-D- glucosa- minide 1,4-beta-linkages in chitin and chitodextrins. 3 Notes on using trace results 6 Catalytic activity: Hydrolysis of 1,4-beta-linkages between N- ace- 3.1 Coverage 6 tylmuramic acid and N-acetyl-D-glucosamine residues in a peptido- 3.2 Known substitutions 6 glycan and between N-acetyl-D-glucosamine residues in chitodex- 3.3 Surface 6 trins. 3.4 Number of contacts 6 Subcellular location: In the lutoids (vacuoles) from rubber latex. 3.5 Annotation 6 Miscellaneous: Two components of hevamine have been isolated: 3.6 Mutation suggestions 6 hevamine A (shown here), the most abundant, and hevamine B. Similarity: Belongs to the glycosyl hydrolase 18 family. Chitinase 4 Appendix 6 class II subfamily. 4.1 File formats 6 About: This Swiss-Prot entry is copyright. It is produced through a 4.2 Color schemes used 6 collaboration between the Swiss Institute of Bioinformatics and the 4.3 Credits 7 EMBL outstation - the European Bioinformatics Institute. There are 1 Lichtarge lab 2006 in 1hvqA can be found in the file called 1hvqA.ranks sorted in the attachment. 2.4 Top ranking residues in 1hvqA 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 1hvqA colored by their importance: bright red and yellow indicate more conser- Fig. 1. Residues 1-136 in 1hvqA colored by their relative importance. (See ved/important residues (see Appendix for the coloring scheme). A Appendix, Fig.9, for the coloring scheme.) Pymol script for producing this figure can be found in the attachment. Fig. 2. Residues 137-273 in 1hvqA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Multiple sequence alignment for 1hvqA For the chain 1hvqA, the alignment 1hvqA.msf (attached) with 217 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 1hvqA.msf. Its statistics, from the alistat program are the following: Fig. 3. Residues in 1hvqA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 217 Total number of residues: 56932 Smallest: 214 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Largest: 273 top 25% of all residues, this time colored according to clusters they Average length: 262.4 belong to. The clusters in Fig.4 are composed of the residues listed Alignment length: 273 in Table 1. Average identity: 39% Most related pair: 99% Table 1. Most unrelated pair: 15% cluster size member Most distant seq: 36% color residues red 64 6,7,8,16,32,36,45,57,63,64 67,68,71,72,74,76,77,78,79 Furthermore, <1% of residues show as conserved in this ali- 80,93,97,101,104,112,113,114 gnment. 115,117,119,120,121,123,124 The alignment consists of 47% eukaryotic ( 13% fungi, 34% 125,126,127,154,155,156,157 plantae), and <1% prokaryotic sequences. (Descriptions of some 158,159,162,163,169,170,175 sequences were not readily available.) The file containing the 176,178,179,180,181,182,183 sequence descriptions can be found in the attachment, under the name 184,185,217,219,220,228,229 1hvqA.descr. 253,255 continued in next column 2.3 Residue ranking in 1hvqA The 1hvqA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) R(14)H A(2) .(4)LTG EMFKVN Table 2. The top 25% of residues in 1hvqA at the interface with NAG.(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 80 G (FW)(HR)(Y)(KE) 255 W (E)(K)(D)(T) 32 F (K)(E)(Q)(D) Fig. 4. Residues in 1hvqA, colored according to the cluster they belong to: 9 Q (Y)(T)(H)(FW) red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The Table 3. List of disruptive mutations for the top 25% of residues in corresponding Pymol script is attached. 1hvqA, that are at the interface with NAG. Table 1. continued cluster size member color residues blue 3 249,250,251 Table 1. Clusters of top ranking residues in 1hvqA. 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. NAG binding site. Table 2 lists the top 25% of residues at the interface with 1hvqNAG3 (nag). The following table (Table 3) sug- gests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 80 G G(99)KE 0.01 3/3 3.94 255 W W(94) 0.05 24/0 3.23 Y(2)RLF V. 32 F F(93) 0.12 5/0 3.99 .(1) Fig. 5. Residues in 1hvqA, at the interface with NAG, colored by their relative importance. The ligand (NAG) is colored green. Atoms further than 30A˚ away Y(1)A from the geometric center of the ligand, as well as on the line of sight to the V(1)TGL ligand were removed. (See Appendix for the coloring scheme for the protein Q chain 1hvqA.) 9 Q Q(72)P 0.25 16/1 3.41 continued in next column Figure 5 shows residues in 1hvqA colored by their importance, at the interface with 1hvqNAG3. 3 NAG binding site. Table 4 lists the top 25% of residues at the interface with 1hvqNAG1 (nag). The following table (Table 5) sug- gests possible disruptive replacements for these residues (see Section 3.6). Table 4. res type subst’s cvg noc/ dist (%) bb (A˚ ) 45 N N(66) 0.22 5/0 3.53 D(22) .(2) S(2) A(1) G(2)VTE 9 Q Q(72)P 0.25 1/1 4.83 R(14)H A(2) .(4)LTG EMFKVN Table 4. The top 25% of residues in 1hvqA at the interface with NAG.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each Fig. 6. Residues in 1hvqA, at the interface with NAG, colored by their relative type in the bracket; noc/bb: number of contacts with the ligand, with the num- importance. The ligand (NAG) is colored green. Atoms further than 30A˚ away ber of contacts realized through backbone atoms given in the bracket; dist: from the geometric center of the ligand, as well as on the line of sight to the distance of closest apporach to the ligand. ) ligand were removed. (See Appendix for the coloring scheme for the protein chain 1hvqA.) Table 5. res type disruptive Table 6. continued mutations res type subst’s cvg noc/ dist 45 N (Y)(H)(FW)(R) (%) bb (A˚ ) 9 Q (Y)(T)(H)(FW) EMFKVN Table 5. List of disruptive mutations for the top 25% of residues in Table 6.