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2Gkg Lichtarge Lab 2006 Pages 1–5 2gkg Evolutionary trace report by report maker April 17, 2009 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 2gkg): Title: Receiver domain from myxococcus xanthus social motility protein frzs Compound: Mol id: 1; molecule: response regulator homolog; chain: a; fragment: receiver domain (residues 1-124); engineered: CONTENTS yes Organism, scientific name: Myxococcus Xanthus; 1 Introduction 1 2gkg contains a single unique chain 2gkgA (122 residues long). 2 Chain 2gkgA 1 2.1 O68522 overview 1 2.2 Multiple sequence alignment for 2gkgA 1 2.3 Residue ranking in 2gkgA 1 2.4 Top ranking residues in 2gkgA and their position on the structure 1 2 CHAIN 2GKGA 2.4.1 Clustering of residues at 25% coverage. 1 2.1 O68522 overview 2.4.2 Possible novel functional surfaces at 25% From SwissProt, id O68522, 100% identical to 2gkgA: coverage. 2 Description: Response regulator homolog. Organism, scientific name: Myxococcus xanthus. 3 Notes on using trace results 3 Taxonomy: Bacteria; Proteobacteria; Deltaproteobacteria; Myxo- 3.1 Coverage 3 coccales; Cystobacterineae; Myxococcaceae; Myxococcus. 3.2 Known substitutions 3 Subcellular location: Cytoplasmic (By similarity). 3.3 Surface 4 3.4 Number of contacts 4 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 2gkgA 4 Appendix 4 For the chain 2gkgA, the alignment 2gkgA.msf (attached) with 677 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 2gkgA.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 3-124 in 2gkgA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Format: MSF Number of sequences: 677 Total number of residues: 78066 Smallest: 92 Largest: 122 Average length: 115.3 Alignment length: 122 Average identity: 38% Most related pair: 98% Most unrelated pair: 10% Most distant seq: 33% Fig. 2. Residues in 2gkgA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of <1% eukaryotic, and 15% prokaryotic 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 2gkgA.descr. 2.3 Residue ranking in 2gkgA The 2gkgA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2gkgA can be found in the file called 2gkgA.ranks sorted in the attachment. 2.4 Top ranking residues in 2gkgA 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 2gkgA 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 2gkgA, colored according to the cluster they belong to: in Table 1. red, followed by blue and yellow are the largest clusters (see Appendix for Table 1. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. cluster size member color residues red 27 6,8,9,10,11,35,38,47,48,52 53,55,56,62,66,70,79,98,99 Table 1. continued 100,101,102,105,106,107,112 cluster size member continued in next column color residues 115 blue 3 22,26,29 2 Table 1. Clusters of top ranking residues in 2gkgA. Table 2. continued res type substitutions(%) cvg E(2)RTVGF 2.4.2 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 2gkgA surface, away from (or Table 2. Residues forming surface ”patch” in 2gkgA. susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 2gkg. It is shown in Fig. 4. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. Table 3. res type disruptive mutations 98 H (E)(T)(D)(Q) 102 Y (K)(Q)(E)(MR) 99 A (KE)(R)(Y)(QD) 100 D (R)(H)(FW)(K) 6 L (R)(Y)(H)(T) 70 K (Y)(FW)(T)(VA) 101 E (H)(FWR)(Y)(CG) 47 P (R)(Y)(K)(E) 79 P (Y)(R)(H)(T) 115 R (TD)(Y)(E)(CG) 48 D (R)(FWH)(Y)(K) Fig. 4. A possible active surface on the chain 2gkgA. The larger cluster it belongs to is shown in blue. Table 3. Disruptive mutations for the surface patch in 2gkgA. The residues belonging to this surface ”patch” are listed in Table Another group of surface residues is shown in Fig.5. The right panel 2, while Table 3 suggests possible disruptive replacements for these shows (in blue) the rest of the larger cluster this surface belongs to. residues (see Section 3.6). Table 2. res type substitutions(%) cvg 98 H G(95)LR(1)QVPHM 0.03 ADE 102 Y F(6)Y(92)CMHV 0.06 99 A A(93)IVC(1)G(2) 0.07 SRTFW 100 D D(91)YKTAV(1) 0.11 S(1)IN(2)RECFHL 6 L L(91)M(2)I(1). 0.12 V(1)FYAHTQ 70 K K(22)R(75)TASQN 0.12 Fig. 5. Another possible active surface on the chain 2gkgA. The larger cluster ECH it belongs to is shown in blue. 101 E E(4)D(83)G(1) 0.16 A(7)QRSFLHYI 47 P P(73)F(5)Y(11) 0.19 The residues belonging to this surface ”patch” are listed in Table A(2)V(2)WI(1) 4, while Table 5 suggests possible disruptive replacements for these H(1)TCDS residues (see Section 3.6). 79 P P(72)V(7)I(12)R 0.20 Table 4. L(2)YA(1)GQM.KF res type substitutions(%) cvg S 105 K K(99)IERL 0.01 115 R R(82)LT(4)A(2) 0.20 106 P P(98)DSAETG 0.02 .(1)HE(1)K(2)MQ 10 S D(97)NP.SGQ 0.05 IVSWC 35 G G(90)VYA(3)F(1) 0.09 48 D D(86)Q(1)S(2) 0.21 SRMILETP H(1)N(2)A(2)K 9 E D(36)E(63).HA 0.13 continued in next column 56 L L(70)M(25)FI(1) 0.14 continued in next column 3 Table 4. continued guide - due to rounding errors these percentages often do not add up res type substitutions(%) cvg to 100%. V(2)T 107 V V(11)F(72)I(6) 0.23 3.3 Surface C(1)Y(4)L(1) To detect candidates for novel functional interfaces, first we look for A(1)ESQTG residues that are solvent accessible (according to DSSP program) by 2 11 D VD(47)E(36)S(8) 0.25 at least 10A˚ , which is roughly the area needed for one water mole- N(3)TIRLQ.YH(1) cule to come in the contact with the residue. Furthermore, we require G that these residues form a “cluster” of residues which have neighbor 55 D .(1)G(7)LM(66) 0.25 within 5A˚ from any of their heavy atoms. S(1)V(5)KE(1) Note, however, that, if our picture of protein evolution is correct, N(7)I(1)THAD(2) the neighboring residues which are not surface accessible might be Q(1)FR equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choo- Table 4. Residues forming surface ”patch” in 2gkgA. sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 3.4 Number of contacts Table 5. 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 105 K (Y)(T)(FW)(CG) the interface, as well as how many of them are realized through the 106 P (R)(Y)(H)(K) backbone atoms (if all or most contacts are through the backbone, 10 S (R)(H)(FW)(K) mutation presumably won’t have strong impact). Two heavy atoms 35 G (R)(K)(E)(H) are considered to be “in contact” if their centers are closer than 5A˚ . 9 E (FWH)(R)(Y)(CG) 3.5 Annotation 56 L (R)(Y)(H)(TK) If the residue annotation is available (either from the pdb file or 107 V (R)(K)(E)(Y) from other sources), another column, with the header “annotation” 11 D (R)(H)(FW)(Y) appears. Annotations carried over from PDB are the following: site 55 D (R)(H)(FW)(Y) (indicating existence of related site record in PDB ), S-S (disulfide bond forming residue), hb (hydrogen bond forming residue, jb (james Table 5.
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