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1Gnz Lichtarge Lab 2006 Pages 1–6 1gnz Evolutionary trace report by report maker May 9, 2010 4.3.1 Alistat 5 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1gnz): Title: Lectin i-b4 from griffonia simplicifolia (gs i-b4)metal free form CONTENTS Compound: Mol id: 1; molecule: lectin; chain: a; other details: lectin i-b4, metal free form 1 Introduction 1 Organism, scientific name: Griffonia Simplicifolia; 1gnz contains a single unique chain 1gnzA (236 residues long). 2 Chain 1gnzA 1 2.1 Q8W1R6 overview 1 2.2 Multiple sequence alignment for 1gnzA 1 2.3 Residue ranking in 1gnzA 1 2.4 Top ranking residues in 1gnzA and their position on 2 CHAIN 1GNZA the structure 2 2.1 Q8W1R6 overview 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Overlap with known functional surfaces at From SwissProt, id Q8W1R6, 100% identical to 1gnzA: 25% coverage. 2 Description: GSI-B4 isolectin (Fragment). 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Griffonia simplicifolia. coverage. 3 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3 Notes on using trace results 4 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Caesalpi- 3.1 Coverage 4 nioideae; Cercideae; Griffonia. 3.2 Known substitutions 4 3.3 Surface 4 3.4 Number of contacts 5 3.5 Annotation 5 2.2 Multiple sequence alignment for 1gnzA 3.6 Mutation suggestions 5 For the chain 1gnzA, the alignment 1gnzA.msf (attached) with 358 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 5 database, and fragments shorter than 75% of the query as well as 4.1 File formats 5 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 5 to this report, under the name of 1gnzA.msf. Its statistics, from the 4.3 Credits 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 4-121 in 1gnzA colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 2. Residues 122-239 in 1gnzA colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 3. Residues in 1gnzA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 358 Total number of residues: 79496 Smallest: 177 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 236 Average length: 222.1 Alignment length: 236 Average identity: 34% Most related pair: 99% Most unrelated pair: 12% Most distant seq: 33% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 59% eukaryotic ( 59% plantae) sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1gnzA.descr. 2.3 Residue ranking in 1gnzA The 1gnzA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1gnzA can be found in the file called 1gnzA.ranks sorted in the attachment. 2.4 Top ranking residues in 1gnzA and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1gnzA, colored according to the cluster they belong to: residues in the protein . Figure 3 shows residues in 1gnzA colored red, followed by blue and yellow are the largest clusters (see Appendix for by their importance: bright red and yellow indicate more conser- the coloring scheme). Clockwise: front, back, top and bottom views. The ved/important residues (see Appendix for the coloring scheme). A corresponding Pymol script is attached. Pymol script for producing this figure can be found in the attachment. in Table 1. 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the top 25% of all residues, this time colored according to clusters they 2 Table 1. cluster size member color residues red 53 7,50,51,52,54,60,69,70,71,73 75,76,77,79,87,88,89,90,91 92,93,94,108,109,110,111,125 126,127,128,129,130,131,144 145,146,147,148,150,154,173 175,177,184,186,204,215,216 217,220,221,233,235 Table 1. Clusters of top ranking residues in 1gnzA. 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. Phosphate ion binding site. Table 2 lists the top 25% of residues at the interface with 1gnzAPO41240 (phosphate ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Fig. 5. Residues in 1gnzA, at the interface with phosphate ion, colored by their relative importance. The ligand (phosphate ion) is colored green. Atoms res type subst’s cvg noc/ dist further than 30A˚ away from the geometric center of the ligand, as well as on ˚ (%) bb (A) the line of sight to the ligand were removed. (See Appendix for the coloring 96 P G(5) 0.18 11/3 3.75 scheme for the protein chain 1gnzA.) P(73)R V(1) S(9) A(4).K N(1) H(1)T Table 2. The top 25% of residues in 1gnzA at the interface with phos- phate 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 number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Fig. 6. A possible active surface on the chain 1gnzA. The larger cluster it belongs to is shown in blue. Table 3. res type disruptive 4, while Table 5 suggests possible disruptive replacements for these mutations residues (see Section 3.6). 96 P (Y)(R)(H)(E) Table 4. Table 3. List of disruptive mutations for the top 25% of residues in res type substitutions(%) cvg 1gnzA, that are at the interface with phosphate ion. 71 F F(95)W(2).STL 0.01 92 F F(97)L(1)TWS. 0.02 177 Y Y(88)F(10)A.ER 0.02 Figure 5 shows residues in 1gnzA colored by their importance, at the 127 V V(93)I(4)NL(1)C 0.05 interface with 1gnzAPO41240. A. 154 S KS(87)P(6)D(1)T 0.05 2.4.3 Possible novel functional surfaces at 25% coverage. One GVRFA group of residues is conserved on the 1gnzA surface, away from (or 144 H R(4)H(86)S(3) 0.06 susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1gnz. It is shown in Fig. 6. The right panel continued in next column shows (in blue) the rest of the larger cluster this surface belongs to. The residues belonging to this surface ”patch” are listed in Table 3 Table 4. continued Table 5. continued res type substitutions(%) cvg res type disruptive .(1)LED(1)PQ(1) mutations G 51 R (D)(T)(E)(Y) 126 A A(88)YG(5)T(3)L 0.07 145 I (Y)(R)(H)(T) FHV.S 7 F (K)(E)(R)(TQ) 70 S S(77)D(9)N(8)T. 0.09 110 L (R)(Y)(T)(K) PAGH 184 L (R)(Y)(H)(K) 57 P P(85)Q(5)R(1) 0.10 54 Y (K)(Q)(R)(E) K(1).A(2)TLISG 96 P (Y)(R)(H)(E) 94 L L(63)I(24)F(1) 0.13 186 V (Y)(E)(R)(K) M(3)V(6).G 69 A (E)(KR)(Y)(D) 235 F F(91)L(3).(2)YP 0.13 58 V (Y)(R)(E)(K) SNVMR 51 R R(74)H(12)W(1)I 0.14 Table 5. Disruptive mutations for the surface patch in 1gnzA. S(1)GLVQ(4)T(1) .FKA Another group of surface residues is shown in Fig.7. The right panel 145 I I(58)V(33)TA 0.14 shows (in blue) the rest of the larger cluster this surface belongs to. L(2)M(1).DFNR 7 F F(84).(6)L(1) 0.16 D(2)VGIEAQY(1)W 110 L I(10)L(70)V(11) 0.17 W.(3)YM(1)PFHS 184 L L(78)M(1)V(5) 0.17 I(7)TF(2)QA(1). ESGY 54 Y Y(79)F(7)H(8)AL 0.18 SIP.CWE 96 P G(5)P(73)RV(1) 0.18 S(9)A(4).KN(1) H(1)T 186 V V(66)A(25)KT 0.21 I(1)L(1)M(2)R.F Fig. 7. Another possible active surface on the chain 1gnzA. The larger cluster 69 A A(67)S(8)V(3) 0.24 it belongs to is shown in blue. T(8)PL(2)YHF(1) .(1)R(2)IQ(1)CG The residues belonging to this surface ”patch” are listed in Table 58 V F(9)I(43)V(33) 0.25 6, while Table 7 suggests possible disruptive replacements for these L(10).(1)MQC residues (see Section 3.6).
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