Pages 1–8 1hjs Evolutionary trace report by report maker April 15, 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 8 4.3.6 Muscle 8 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 1hjs): Title: Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and ph optimum. Compound: Mol id: 1; molecule: beta-1,4-galactanase; chain: a, b, c, d; ec: 3.2.1.89; engineered: yes; other details: 2-n-acetyl-beta-d- glucose(residue 601) linked to asn 111 in the four molecules Organism, scientific name: Thielavia Heterothallica; 1hjs contains a single unique chain 1hjsA (332 residues long) and CONTENTS its homologues 1hjsD, 1hjsC, and 1hjsB. 1 Introduction 1 2 CHAIN 1HJSA 2.1 P83692 overview 2 Chain 1hjsA 1 2.1 P83692 overview 1 From SwissProt, id P83692, 96% identical to 1hjsA: 2.2 Multiple sequence alignment for 1hjsA 1 Description: Arabinogalactan endo-1,4-beta-galactosidase (EC 2.3 Residue ranking in 1hjsA 1 3.2.1.89) (Endo-1,4- beta-galactanase) (Galactanase). 2.4 Top ranking residues in 1hjsA and their position on Organism, scientific name: Thielavia heterothallica (Mycelio- the structure 2 phthora thermophila). 2.4.1 Clustering of residues at 25% coverage. 2 Taxonomy: Eukaryota; Fungi; Ascomycota; Pezizomycotina; 2.4.2 Overlap with known functional surfaces at Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; 25% coverage. 2 Corynascus. 2.4.3 Possible novel functional surfaces at 25% Catalytic activity: Endohydrolysis of 1,4-beta-D-galactosidic linka- coverage. 4 ges in arabinogalactans. Miscellaneous: Has a pH range of 5.5-8.5 with optimum of 7.0; and 3 Notes on using trace results 6 a temperature optimum of 65 degrees Celsius at pH 6.5. 3.1 Coverage 6 Similarity: Belongs to the glycosyl hydrolase 53 family. 3.2 Known substitutions 6 About: This Swiss-Prot entry is copyright. It is produced through a 3.3 Surface 6 collaboration between the Swiss Institute of Bioinformatics and the 3.4 Number of contacts 6 EMBL outstation - the European Bioinformatics Institute. There are 3.5 Annotation 7 no restrictions on its use as long as its content is in no way modified 3.6 Mutation suggestions 7 and this statement is not removed. 4 Appendix 7 2.2 Multiple sequence alignment for 1hjsA 4.1 File formats 7 For the chain 1hjsA, the alignment 1hjsA.msf (attached) with 93 4.2 Color schemes used 7 sequences was used. The alignment was downloaded from the HSSP 4.3 Credits 7 database, and fragments shorter than 75% of the query as well as 1 Lichtarge lab 2006 2.4 Top ranking residues in 1hjsA 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 1hjsA 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 1-166 in 1hjsA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 2. Residues 167-332 in 1hjsA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1hjsA.msf. Its statistics, from the Fig. 3. Residues in 1hjsA, colored by their relative importance. Clockwise: alistat program are the following: front, back, top and bottom views. Format: MSF Number of sequences: 93 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 28259 top 25% of all residues, this time colored according to clusters they Smallest: 92 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 332 in Table 1. Average length: 303.9 Alignment length: 332 Table 1. Average identity: 36% cluster size member Most related pair: 99% color residues Most unrelated pair: 0% red 70 6,8,10,11,45,47,49,50,52,55 Most distant seq: 38% 58,77,78,79,80,81,82,83,84 86,87,88,89,92,95,97,98,105 112,113,127,130,131,132,133 Furthermore, <1% of residues show as conserved in this ali- 134,135,139,141,156,160,163 gnment. 164,165,175,178,179,180,182 The alignment consists of 4% eukaryotic ( 4% fungi), and 17% 192,206,207,209,210,212,214 prokaryotic sequences. (Descriptions of some sequences were not 215,217,239,245,248,272,273 readily available.) The file containing the sequence descriptions can 294,295,296,297,298,300,307 be found in the attachment, under the name 1hjsA.descr. blue 6 16,19,66,68,69,73 yellow 3 36,40,42 2.3 Residue ranking in 1hjsA green 2 290,292 purple 2 120,124 The 1hjsA 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 1hjsA can be found in the file called 1hjsA.ranks sorted in the attachment. 2 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 73 G (R)(FKWH)(E)(M) 42 N (FYWH)(R)(TVA)(CG) Table 3. List of disruptive mutations for the top 25% of residues in 1hjsA, that are at the interface with PEG. Fig. 4. Residues in 1hjsA, 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. Table 1. continued cluster size member color residues Table 1. Clusters of top ranking residues in 1hjsA. 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. Fig. 5. Residues in 1hjsA, at the interface with PEG, colored by their relative A˚ PEG binding site. By analogy with 1hjsB – 1hjsBPEG801 inter- importance. The ligand (PEG) is colored green. Atoms further than 30 away from the geometric center of the ligand, as well as on the line of sight to the face. Table 2 lists the top 25% of residues at the interface with ligand were removed. (See Appendix for the coloring scheme for the protein 1hjsBPEG801 (peg). The following table (Table 3) suggests possible chain 1hjsA.) disruptive replacements for these residues (see Section 3.6). Table 2. Figure 5 shows residues in 1hjsA colored by their importance, at the res type subst’s cvg noc/ dist antn interface with 1hjsBPEG801. (%) bb (A˚ ) Sulfate ion binding site. Table 4 lists the top 25% of residues 73 G G(87) 0.10 8/8 3.04 at the interface with 1hjsASO4701 (sulfate ion). The following table .(3) (Table 5) suggests possible disruptive replacements for these residues N(7) (see Section 3.6). D(2) Table 4. 42 N D(10) 0.14 17/7 3.58 site res type subst’s cvg noc/ dist antn N(84) (%) bb (A˚ ) .(3) 98 W W(97) 0.01 12/0 3.02 site T(1) .(2) 50 V V(58) 0.16 4/0 3.74 Table 2. The top 25% of residues in 1hjsA at the interface with continued in next column PEG.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each 3 Table 4. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) N(27) .(2) H(7) G(1) I(1) T(1) Q(1) 112 Y H(22) 0.17 6/1 3.44 Y(63) .(3) F(9) S(1) Table 4. The top 25% of residues in 1hjsA at the interface with sulfate ion.(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. ) Fig. 6. Residues in 1hjsA, at the interface with sulfate ion, colored by their relative importance. The ligand (sulfate ion) is colored green. Atoms further Table 5. than 30A˚ away from the geometric center of the ligand, as well as on the line res type disruptive of sight to the ligand were removed. (See Appendix for the coloring scheme mutations for the protein chain 1hjsA.) 98 W (KE)(TQD)(SNCG)(R) 50 V (YER)(K)(H)(D) 112 Y (K)(Q)(M)(E) Table 7. res type disruptive mutations Table 5. List of disruptive mutations for the top 25% of residues in 1hjsA, that are at the interface with sulfate ion. 42 N (FYWH)(R)(TVA)(CG) Table 7. List of disruptive mutations for the top 25% of residues in 1hjsA, Figure 6 shows residues in 1hjsA colored by their importance, at the that are at the interface with sulfate ion.