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1A7w Lichtarge Lab 2006 Pages 1–6 1a7w Evolutionary trace report by report maker July 11, 2010 4.3.1 Alistat 5 4.3.2 CE 5 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 1a7w): Title: Crystal structure of the histone hmfb from methanothermus fervidus Compound: Mol id: 1; molecule: histone hmfb; chain: a; enginee- red: yes Organism, scientific name: Methanothermus Fervidus; 1a7w contains a single unique chain 1a7wA (68 residues long). CONTENTS 1 Introduction 1 2 CHAIN 1A7WA 2.1 P19267 overview 2 Chain 1a7wA 1 From SwissProt, id P19267, 100% identical to 1a7wA: 2.1 P19267 overview 1 Description: DNA binding protein HMf-2 (Archaeal histone B). 2.2 Multiple sequence alignment for 1a7wA 1 Organism, scientific name: Methanothermus fervidus. 2.3 Residue ranking in 1a7wA 1 Taxonomy: Archaea; Euryarchaeota; Methanobacteria; Methanob- 2.4 Top ranking residues in 1a7wA and their position on acteriales; Methanothermaceae; Methanothermus. the structure 1 Function: Binds and compact DNA (95 to 150 base pairs) to form 2.4.1 Clustering of residues at 25% coverage. 2 nucleosome-like structures that contain positive DNA supercoils. 2.4.2 Overlap with known functional surfaces at Increases the resistance of DNA to thermal denaturation. 25% coverage. 2 Subunit: Homodimer or heterodimer of HMf-1 and HMf-2. 2.4.3 Possible novel functional surfaces at 25% Similarity: Belongs to the archaeal histone HMF family. coverage. 3 About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the 3 Notes on using trace results 4 EMBL outstation - the European Bioinformatics Institute. There are 3.1 Coverage 4 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 5 3.5 Annotation 5 2.2 Multiple sequence alignment for 1a7wA 3.6 Mutation suggestions 5 For the chain 1a7wA, the alignment 1a7wA.msf (attached) with 104 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 1a7wA.msf. Its statistics, from the 4.3 Credits 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-68 in 1a7wA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Format: MSF Number of sequences: 104 Total number of residues: 6751 Smallest: 53 Largest: 68 Average length: 64.9 Alignment length: 68 Average identity: 43% Most related pair: 99% Most unrelated pair: 13% Most distant seq: 37% Furthermore, <1% of residues show as conserved in this ali- Fig. 2. Residues in 1a7wA, colored by their relative importance. Clockwise: gnment. front, back, top and bottom views. The alignment consists of 12% eukaryotic ( 2% vertebrata, <1% arthropoda, 1% fungi, 3% plantae), 8% prokaryotic, and 58% archaean sequences. (Descriptions of some sequences were not rea- dily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1a7wA.descr. 2.3 Residue ranking in 1a7wA The 1a7wA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1a7wA can be found in the file called 1a7wA.ranks sorted in the attachment. 2.4 Top ranking residues in 1a7wA 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 1a7wA 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 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 Fig. 3. Residues in 1a7wA, colored according to the cluster they belong to: in Table 1. red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The Table 1. corresponding Pymol script is attached. cluster size member color residues red 8 43,47,50,52,53,54,59,63 2.4.2 Overlap with known functional surfaces at 25% coverage. blue 8 4,6,7,10,12,19,20,24 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 1a7wA. Interface with 1a7wA1.Table 2 lists the top 25% of residues at the interface with 1a7wA1. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). 2 Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 54 T T(97) 0.04 33/11 3.28 V(1)H 24 A A(92) 0.07 30/18 3.49 G(1)V S(3)I 33 E S(20) 0.09 11/3 4.31 E(72) G(1)C T(3)V 4 P P(90) 0.10 7/0 3.79 V(1) G(3)ST .(1) 53 K K(88) 0.13 35/15 3.21 R(6)VTS ED 19 R K(22) 0.15 54/31 2.87 R(71)GI STN(1)A 10 R R(93) 0.18 18/2 3.02 E(1) A(1)VKI 7 P N(22) 0.19 19/8 3.57 P(55) A(11) V(1) S(3) T(3). 20 V I(28) 0.23 20/14 3.83 V(65) A(1) L(1)GP 12 I M(24) 0.25 15/6 3.89 A(15) I(30) L(25) F(1)VC Table 2. The top 25% of residues in 1a7wA at the interface with 1a7wA1. (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. ) Table 3. res type disruptive mutations 54 T (K)(R)(Q)(M) 24 A (R)(K)(YE)(H) 33 E (H)(R)(FW)(Y) 4 P (R)(Y)(H)(K) continued in next column 3 Table 3. continued res type disruptive mutations 53 K (Y)(FW)(T)(H) 19 R (YD)(E)(T)(FW) 10 R (Y)(T)(D)(ECG) 7 P (R)(Y)(H)(K) 20 V (R)(Y)(KE)(H) 12 I (R)(Y)(H)(TKE) Table 3. List of disruptive mutations for the top 25% of residues in 1a7wA, that are at the interface with 1a7wA1. Fig. 5. A possible active surface on the chain 1a7wA. Table 4. continued res type substitutions(%) cvg 6 A A(91)TNG(1)E 0.12 S(1).D 19 R K(22)R(71)GIST 0.15 N(1)A 10 R R(93)E(1)A(1)VK 0.18 I 7 P N(22)P(55)A(11) 0.19 V(1)S(3)T(3). 20 V I(28)V(65)A(1) 0.23 L(1)GP Fig. 4. Residues in 1a7wA, at the interface with 1a7wA1, colored by their 12 I M(24)A(15)I(30) 0.25 relative importance. 1a7wA1 is shown in backbone representation (See L(25)F(1)VC Appendix for the coloring scheme for the protein chain 1a7wA.) Table 4. Residues forming surface ”patch” in 1a7wA. Figure 4 shows residues in 1a7wA colored by their importance, at the interface with 1a7wA1. Table 5. 2.4.3 Possible novel functional surfaces at 25% coverage. One res type disruptive group of residues is conserved on the 1a7wA surface, away from (or mutations susbtantially larger than) other functional sites and interfaces reco- 24 A (R)(K)(YE)(H) gnizable in PDB entry 1a7w. It is shown in Fig. 5. The residues 4 P (R)(Y)(H)(K) belonging to this surface ”patch” are listed in Table 4, while Table 6 A (R)(K)(Y)(H) 5 suggests possible disruptive replacements for these residues (see 19 R (YD)(E)(T)(FW) Section 3.6). 10 R (Y)(T)(D)(ECG) Table 4. 7 P (R)(Y)(H)(K) res type substitutions(%) cvg 20 V (R)(Y)(KE)(H) 24 A A(92)G(1)VS(3)I 0.07 12 I (R)(Y)(H)(TKE) 4 P P(90)V(1)G(3)ST 0.10 .(1) Table 5. Disruptive mutations for the surface patch in 1a7wA. continued in next column Another group of surface residues is shown in Fig.6. The residues 4 in a chain], according to trace. The ET results are presented in the form of a table, usually limited to top 25% percent of residues (or to some nearby percentage), sorted by the strength of the presumed evolutionary pressure. (I.e., the smaller the coverage, the stronger the pressure on the residue.) Starting from the top of that list, mutating a couple of residues should affect the protein somehow, with the exact effects to be determined experimentally.
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