Pages 1–12 2jgu Evolutionary trace report by report maker July 23, 2010 4.3.1 Alistat 11 4.3.2 CE 11 4.3.3 DSSP 11 4.3.4 HSSP 11 4.3.5 LaTex 11 4.3.6 Muscle 11 4.3.7 Pymol 12 4.4 Note about ET Viewer 12 4.5 Citing this work 12 4.6 About report maker 12 4.7 Attachments 12 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2jgu): Title: Crystal structure of dna-directed dna polymerase Compound: Mol id: 1; molecule: dna polymerase; synonym: pfu polymerase, dna polymerase pfu; chain: a; ec: 2.7.7.7; engineered: yes Organism, scientific name: Pyrococcus Furiosus 2jgu contains a single unique chain 2jguA (712 residues long). CONTENTS 2 CHAIN 2JGUA 1 Introduction 1 2.1 P61876 overview 2 Chain 2jguA 1 From SwissProt, id P61876, 90% identical to 2jguA: 2.1 P61876 overview 1 Description: DNA polymerase (EC 2.7.7.7) (Pwo polymerase). 2.2 Multiple sequence alignment for 2jguA 1 Organism, scientific name: Pyrococcus woesei. 2.3 Residue ranking in 2jguA 1 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 2.4 Top ranking residues in 2jguA and their position on les; Thermococcaceae; Pyrococcus. the structure 2 Function: In addition to polymerase activity, this DNA polymerase 2.4.1 Clustering of residues at 25% coverage. 2 exhibits 3’ to 5’ exonuclease activity. 2.4.2 Overlap with known functional surfaces at Catalytic activity: Deoxynucleoside triphosphate + DNA(n) = 25% coverage. 3 diphosphate + DNA(n+1). 2.4.3 Possible novel functional surfaces at 25% Subunit: Monomer. coverage. 4 Similarity: Belongs to the DNA polymerase type-B family. About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 10 collaboration between the Swiss Institute of Bioinformatics and the 3.1 Coverage 10 EMBL outstation - the European Bioinformatics Institute. There are 3.2 Known substitutions 10 no restrictions on its use as long as its content is in no way modified 3.3 Surface 10 and this statement is not removed. 3.4 Number of contacts 10 3.5 Annotation 10 2.2 Multiple sequence alignment for 2jguA 3.6 Mutation suggestions 11 For the chain 2jguA, the alignment 2jguA.msf (attached) with 79 sequences was used. The alignment was assembled through combi- 4 Appendix 11 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 11 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 11 report, under the name of 2jguA.msf. Its statistics, from the alistat 4.3 Credits 11 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-237 in 2jguA colored by their relative importance. (See Fig. 3. Residues 475-758 in 2jguA colored by their relative importance. (See Appendix, Fig.13, for the coloring scheme.) Appendix, Fig.13, for the coloring scheme.) 2.4 Top ranking residues in 2jguA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 4 shows residues in 2jguA 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. 2. Residues 238-474 in 2jguA colored by their relative importance. (See Appendix, Fig.13, for the coloring scheme.) Format: MSF Number of sequences: 79 Total number of residues: 53686 Smallest: 566 Largest: 712 Average length: 679.6 Alignment length: 712 Average identity: 29% Most related pair: 99% Most unrelated pair: 17% Most distant seq: 32% Furthermore, 1% of residues show as conserved in this alignment. The alignment consists of 31% eukaryotic ( 11% vertebrata, 11% Fig. 4. Residues in 2jguA, colored by their relative importance. Clockwise: fungi, 2% plantae), 12% prokaryotic, 39% archaean, and 17% viral front, back, top and bottom views. 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 2jguA.descr. 2.4.1 Clustering of residues at 25% coverage. Fig. 5 shows the top 25% of all residues, this time colored according to clusters they 2.3 Residue ranking in 2jguA belong to. The clusters in Fig.5 are composed of the residues listed The 2jguA sequence is shown in Figs. 1–3, with each residue colored in Table 1. according to its estimated importance. The full listing of residues in 2jguA can be found in the file called 2jguA.ranks sorted in the attachment. 2 Table 1. continued cluster size member color residues yellow 8 679,680,681,683,684,700,702 703 green 7 617,619,621,661,729,732,733 purple 5 19,203,204,254,255 azure 2 343,345 Table 1. Clusters of top ranking residues in 2jguA. 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. Manganese (ii) ion binding site. Table 2 lists the top 25% of resi- dues at the interface with 2jguAMN1758 (manganese (ii) ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) Fig. 5. Residues in 2jguA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for 343 D D(26) 0.20 3/0 3.39 site the coloring scheme). Clockwise: front, back, top and bottom views. The Q(6) corresponding Pymol script is attached. C(5) E(7) Y(13) Table 1. R(34) cluster size member F(6) color residues red 120 37,39,111,113,114,119,123 Table 2. The top 25% of residues in 2jguA at the interface with manga- 329,332,348,349,350,352,353 nese (ii) ion.(Field names: res: residue number in the PDB entry; type: amino 356,357,361,368,369,385,387 acid type; substs: substitutions seen in the alignment; with the percentage of 388,390,393,396,397,398,401 each type in the bracket; noc/bb: number of contacts with the ligand, with 403,404,405,406,408,409,410 the number of contacts realized through backbone atoms given in the bracket; 411,412,413,414,418,419,420 dist: distance of closest apporach to the ligand. ) 421,422,423,448,450,454,457 458,461,465,480,481,482,483 484,485,486,487,488,490,491 Table 3. 492,493,494,495,496,497,498 res type disruptive 499,503,504,505,506,507,510 mutations 511,512,513,514,515,518,519 343 D (R)(FW)(H)(VA) 522,537,539,540,541,542,543 544,546,569,572,575,576,578 Table 3. List of disruptive mutations for the top 25% of residues in 2jguA, 579,581,582,584,587,588,589 that are at the interface with manganese (ii) ion. 590,591,592,593,594,595,596 597,607,608,609,610,632,744 Figure 6 shows residues in 2jguA colored by their importance, at the 745 interface with 2jguAMN1758. blue 33 140,141,142,143,144,187,191 Manganese (ii) ion binding site. Table 4 lists the top 25% of resi- 194,207,208,209,210,214,215 dues at the interface with 2jguAMN1759 (manganese (ii) ion). The 217,218,222,223,259,260,261 following table (Table 5) suggests possible disruptive replacements 270,273,275,278,283,287,308 for these residues (see Section 3.6). 311,315,316,319,322 Table 4. continued in next column res type subst’s cvg noc/ dist antn (%) bb (A˚ ) continued in next column 3 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. ) Table 5. res type disruptive mutations 315 D (R)(FWH)(Y)(VCAG) 143 E (FWH)(Y)(R)(CG) 141 D (R)(H)(FW)(K) 311 Y (K)(EQ)(M)(R) 142 I (R)(Y)(H)(KE) Table 5. List of disruptive mutations for the top 25% of residues in 2jguA, that are at the interface with manganese (ii) ion. Fig. 6. Residues in 2jguA, at the interface with manganese (ii) ion, colored by their relative importance. The ligand (manganese (ii) ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 2jguA.) Table 4. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 315 D D(98) 0.03 4/0 2.03 N(1) 143 E E(88) 0.05 4/0 2.14 site K(8) S(1) V(1) 141 D D(87) 0.10 4/0 2.23 site A(2) S(7) G(1) Fig. 7. Residues in 2jguA, at the interface with manganese (ii) ion, colored N(1) by their relative importance. The ligand (manganese (ii) ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well 311 Y Y(87) 0.10 3/0 4.22 as on the line of sight to the ligand were removed. (See Appendix for the H(8) coloring scheme for the protein chain 2jguA.) L(1) N(1) W(1) Figure 7 shows residues in 2jguA colored by their importance, at the 142 I I(84) 0.17 3/3 3.31 site interface with 2jguAMN1759.