Pages 1–5 2zib Evolutionary trace report by report maker September 10, 2008 4.3.1 Alistat 5 4.3.2 CE 5 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 2zib): Title: Crystal structure analysis of calcium-independent type ii antifreeze protein Compound: Mol id: 1; molecule: type ii antifreeze protein; chain: a; engineered: yes Organism, scientific name: Brachyopsis Rostratus; 2zib contains a single unique chain 2zibA (130 residues long). CONTENTS 1 Introduction 1 2 CHAIN 2ZIBA 2.1 P05140 overview 2 Chain 2zibA 1 From SwissProt, id P05140, 68% identical to 2zibA: 2.1 P05140 overview 1 Description: Type II antifreeze protein precursor (AFP). 2.2 Multiple sequence alignment for 2zibA 1 Organism, scientific name: Hemitripterus americanus (Sea raven). 2.3 Residue ranking in 2zibA 1 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 2.4 Top ranking residues in 2zibA and their position on Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; the structure 1 Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Scor- 2.4.1 Clustering of residues at 25% coverage. 2 paeniformes; Cottoidei; Hemitripteridae; Hemitripterus. 2.4.2 Overlap with known functional surfaces at Function: Antifreeze proteins lower the blood freezing point. 25% coverage. 2 Subcellular location: Secreted. 2.4.3 Possible novel functional surfaces at 25% Similarity: Contains 1 C-type lectin domain. coverage. 3 About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 3 collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are 3.1 Coverage 3 no restrictions on its use as long as its content is in no way modified 3.2 Known substitutions 4 and this statement is not removed. 3.3 Surface 4 3.4 Number of contacts 4 2.2 Multiple sequence alignment for 2zibA 3.5 Annotation 4 3.6 Mutation suggestions 4 For the chain 2zibA, the alignment 2zibA.msf (attached) with 28 sequences was used. The alignment was assembled through combi- 4 Appendix 4 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 4 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 5 report, under the name of 2zibA.msf. Its statistics, from the alistat 4.3 Credits 5 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 4-133 in 2zibA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Format: MSF Number of sequences: 28 Total number of residues: 3579 Smallest: 120 Largest: 130 Average length: 127.8 Alignment length: 130 Average identity: 36% Most related pair: 98% Most unrelated pair: 21% Most distant seq: 33% Fig. 2. Residues in 2zibA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, 5% of residues show as conserved in this alignment. The alignment consists of 96% eukaryotic ( 85% vertebrata) 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 2zibA.descr. 2.3 Residue ranking in 2zibA The 2zibA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2zibA can be found in the file called 2zibA.ranks sorted in the attachment. 2.4 Top ranking residues in 2zibA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 2zibA 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. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Fig. 3. Residues in 2zibA, colored according to the cluster they belong to: Table 1. red, followed by blue and yellow are the largest clusters (see Appendix for cluster size member the coloring scheme). Clockwise: front, back, top and bottom views. The color residues corresponding Pymol script is attached. red 33 10,14,17,21,22,31,34,35,38 44,45,47,53,56,57,66,67,68 69,78,80,82,90,91,96,104,115 116,117,120,128,129,130 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. Table 1. Clusters of top ranking residues in 2zibA. Sulfate ion binding site. Table 2 lists the top 25% of residues at the interface with 2zibASO4501 (sulfate ion). The following table 2 (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 82 D D(85) 0.18 1/1 4.75 E(7) R(3) N(3) 44 H H(78) 0.21 15/0 2.66 Q(7) V(3) N(7) S(3) Table 2. The top 25% of residues in 2zibA 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. 4. Residues in 2zibA, at the interface with sulfate ion, colored by their Table 3. relative importance. The ligand (sulfate ion) is colored green. Atoms further 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 2zibA.) 82 D (FW)(HR)(Y)(VCAG) 44 H (E)(TD)(M)(Q) Table 3. List of disruptive mutations for the top 25% of residues in 2zibA, that are at the interface with sulfate ion. Figure 4 shows residues in 2zibA colored by their importance, at the interface with 2zibASO4501. 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 2zibA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 2zib. It is shown in Fig. 5. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. Fig. 5. A possible active surface on the chain 2zibA. The larger cluster it The residues belonging to this surface ”patch” are listed in Table belongs to is shown in blue. 4, while Table 5 suggests possible disruptive replacements for these residues (see Section 3.6). Table 4. continued Table 4. res type substitutions(%) cvg antn res type substitutions(%) cvg antn N(3) 80 W W(100) 0.05 78 W F(50)W(46)Y(3) 0.19 120 C C(92)L(7) 0.07 S-S 35 E E(78)Q(10)K(7) 0.20 91 W W(92)I(7) 0.08 S(3) 14 W W(96)Y(3) 0.09 44 H H(78)Q(7)V(3) 0.21 31 W W(96)Y(3) 0.10 N(7)S(3) 96 P P(85).(7)F(7) 0.12 116 D N(71)D(10)A(3) 0.21 10 C C(89)V(7)I(3) 0.15 S-S V(7)R(7) 129 A K(64)Q(25)E(3) 0.17 117 D D(67)S(3)T(7) 0.22 A(7) P(7)N(14) 82 D D(85)E(7)R(3) 0.18 90 T N(60)F(10)A(7) 0.23 continued in next column T(7)Q(3)I(7) continued in next column 3 Table 4. continued guide - due to rounding errors these percentages often do not add up res type substitutions(%) cvg antn to 100%. D(3) 130 K K(64)R(10)E(7) 0.25 3.3 Surface I(10)M(7) To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by 2 Table 4. Residues forming surface ”patch” in 2zibA. at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require that these residues form a “cluster” of residues which have neighbor A˚ Table 5. within 5 from any of their heavy atoms. Note, however, that, if our picture of protein evolution is correct, res type disruptive the neighboring residues which are not surface accessible might be mutations equally important in maintaining the interaction specificity - they 80 W (KE)(TQD)(SNCRG)(M) should not be automatically dropped from consideration when choo- 120 C (R)(KE)(H)(FYQWD) sing the set for mutagenesis. (Especially if they form a cluster with 91 W (KE)(T)(QDR)(SCG) the surface residues.) 14 W (K)(E)(Q)(D) 31 W (K)(E)(Q)(D) 3.4 Number of contacts 96 P (R)(Y)(T)(H) Another column worth noting is denoted “noc/bb”; it tells the num- 10 C (R)(KE)(H)(Y) ber of contacts heavy atoms of the residue in question make across 129 A (Y)(H)(R)(E) the interface, as well as how many of them are realized through the 82 D (FW)(HR)(Y)(VCAG) backbone atoms (if all or most contacts are through the backbone, 78 W (K)(E)(Q)(D) mutation presumably won't have strong impact).