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1Xg6 Lichtarge Lab 2006 Pages 1–5 1xg6 Evolutionary trace report by report maker May 21, 2010 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1xg6): Title: The crystal structure of the p1 mutant (leu to arg)of a winged bean chymotrypsin inhibitor(kunitz)solved at 2.15a resolution Compound: Mol id: 1; molecule: chymotrypsin inhibitor 3; chain: a; synonym: winged bean chymotrypsin inhibitor, wci-3; engineered: yes; mutation: yes Organism, scientific name: Psophocarpus Tetragonolobus; 1xg6 contains a single unique chain 1xg6A (179 residues long). CONTENTS 2 CHAIN 1XG6A 1 Introduction 1 2.1 P10822 overview From SwissProt, id P10822, 98% identical to 1xg6A: 2 Chain 1xg6A 1 Description: Chymotrypsin inhibitor 3 precursor (WCI-3). 2.1 P10822 overview 1 Organism, scientific name: Psophocarpus tetragonolobus (Goa 2.2 Multiple sequence alignment for 1xg6A 1 bean) (Asparagus bean). 2.3 Residue ranking in 1xg6A 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 1xg6A and their position on Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core the structure 2 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 2.4.1 Clustering of residues at 25% coverage. 2 deae; Phaseoleae; Psophocarpus. 2.4.2 Possible novel functional surfaces at 25% Function: Inhibits alpha-chymotrypsin at the molar ratio of 1:2 in coverage. 2 state of 1:1. Similarity: Belongs to the leguminous Kunitz-type inhibitor family. 3 Notes on using trace results 3 About: This Swiss-Prot entry is copyright. It is produced through a 3.1 Coverage 3 collaboration between the Swiss Institute of Bioinformatics and the 3.2 Known substitutions 3 EMBL outstation - the European Bioinformatics Institute. There are 3.3 Surface 4 no restrictions on its use as long as its content is in no way modified 3.4 Number of contacts 4 and this statement is not removed. 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 1xg6A 4 Appendix 4 For the chain 1xg6A, the alignment 1xg6A.msf (attached) with 42 4.1 File formats 4 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 4 database, and fragments shorter than 75% of the query as well as 4.3 Credits 4 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 4 to this report, under the name of 1xg6A.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 0-178 in 1xg6A colored by their relative importance. (See Appendix, Fig.5, for the coloring scheme.) Format: MSF Number of sequences: 42 Total number of residues: 7152 Smallest: 158 Largest: 179 Average length: 170.3 Alignment length: 179 Average identity: 40% Most related pair: 99% Fig. 2. Residues in 1xg6A, colored by their relative importance. Clockwise: Most unrelated pair: 21% front, back, top and bottom views. Most distant seq: 35% Furthermore, 2% of residues show as conserved in this alignment. The alignment consists of 73% eukaryotic ( 73% 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 1xg6A.descr. 2.3 Residue ranking in 1xg6A The 1xg6A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1xg6A can be found in the file called 1xg6A.ranks sorted in the attachment. 2.4 Top ranking residues in 1xg6A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 1xg6A 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. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the Fig. 3. Residues in 1xg6A, colored according to the cluster they belong to: top 25% of all residues, this time colored according to clusters they red, followed by blue and yellow are the largest clusters (see Appendix for belong to. The clusters in Fig.3 are composed of the residues listed the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. in Table 1. Table 1. Table 1. continued cluster size member cluster size member color residues color residues red 43 7,9,12,15,17,18,19,21,22,24 49,50,51,54,58,63,72,120,133 25,32,33,40,42,44,45,47,48 134,135,137,138,151,152,156 continued in next column 162,163,164,165,170,173,175 continued in next column 2 Table 1. continued Table 2. continued cluster size member res type substitutions(%) cvg antn color residues R(2) 177 51 S A(9)S(64)D(16) 0.16 E(9) Table 1. Clusters of top ranking residues in 1xg6A. 42 E E(88)L(2).(2) 0.17 S(7) 170 P P(85)V(2)N(7) 0.18 2.4.2 Possible novel functional surfaces at 25% coverage. One A(4) group of residues is conserved on the 1xg6A surface, away from (or 137 Y Y(42)F(47)H(7) 0.20 susbtantially larger than) other functional sites and interfaces reco- S(2) gnizable in PDB entry 1xg6. It is shown in Fig. 4. The right panel 177 K K(78)D(7).(7) 0.20 shows (in blue) the rest of the larger cluster this surface belongs to. R(2)E(4) 24 L L(78)I(7)V(9) 0.21 M(4) 50 R Q(73)R(9)K(9) 0.21 L(7) 25 P P(73)S(19)E(2) 0.22 V(4) 17 N N(76)S(11)P(9) 0.23 A(2) 165 V V(73)L(21)A(2) 0.23 G(2) 7 L L(38)V(59)I(2) 0.24 71 F I(16)F(61)V(7) 0.25 D(7)T(2)N(2) Fig. 4. A possible active surface on the chain 1xg6A. The larger cluster it G(2) belongs to is shown in blue. 164 V V(64)I(11)N(7) 0.25 A(14)L(2) The residues belonging to this surface ”patch” are listed in Table Table 2. Residues forming surface ”patch” in 1xg6A. 2, while Table 3 suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Table 3. res type substitutions(%) cvg antn res type disruptive 9 D D(100) 0.02 mutations 45 P P(100) 0.02 9 D (R)(FWH)(KYVCAG)(TQM) 133 Y Y(100) 0.02 45 P (YR)(TH)(SKECG)(FQWD) 22 Y Y(97)T(2) 0.04 133 Y (K)(QM)(NEVLAPIR)(D) 58 G G(97)A(2) 0.04 22 Y (K)(QM)(R)(NELPI) 138 C C(92)Y(7) 0.06 S-S 58 G (KER)(QHD)(FYMW)(N) 49 V V(88)L(9)A(2) 0.07 138 C (K)(ER)(QM)(D) 72 I L(4)I(95) 0.09 49 V (YR)(KE)(H)(QD) 19 G G(85)A(7)V(7) 0.11 72 I (YR)(TH)(SKECG)(FQWD) 12 G G(92)D(4)S(2) 0.12 19 G (KER)(QHD)(Y)(FMW) 44 C C(88)Y(2)E(7) 0.12 S-S 12 G (R)(K)(FWH)(EQM) D(2) 44 C (R)(K)(FWH)(QM) 162 R R(83)Y(7)P(7) 0.13 162 R (D)(TE)(Y)(SCG) A(2) 134 K (Y)(FTW)(SVCAG)(H) 134 K K(95)N(4) 0.14 156 D (R)(FW)(H)(YCG) 156 D D(73)N(9)H(7) 0.14 40 G (KER)(FWH)(YD)(QM) .(7)S(2) 18 G (KER)(FWH)(YQMD)(NLPI) 40 G G(88)E(7)V(2) 0.15 51 S (R)(K)(H)(FW) R(2) 42 E (H)(FW)(R)(Y) 18 G G(90)A(4)D(2) 0.16 170 P (Y)(R)(H)(TE) continued in next column continued in next column 3 Table 3. continued 3.4 Number of contacts res type disruptive Another column worth noting is denoted “noc/bb”; it tells the num- mutations ber of contacts heavy atoms of the residue in question make across 137 Y (K)(Q)(M)(E) the interface, as well as how many of them are realized through the 177 K (Y)(FW)(T)(VCAG) backbone atoms (if all or most contacts are through the backbone, 24 L (Y)(R)(H)(T) mutation presumably won’t have strong impact). Two heavy atoms 50 R (T)(Y)(D)(SCG) are considered to be “in contact” if their centers are closer than 5A˚ . 25 P (R)(Y)(H)(K) 17 N (Y)(H)(R)(FW) 3.5 Annotation 165 V (R)(KYE)(H)(QD) 7 L (YR)(H)(T)(KE) If the residue annotation is available (either from the pdb file or 71 F (K)(E)(R)(Q) from other sources), another column, with the header “annotation” 164 V (Y)(R)(E)(K) appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide bond forming residue), hb (hydrogen bond forming residue, jb (james Table 3.
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