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1Ki1 Lichtarge Lab 2006

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1Ki1 Lichtarge Lab 2006 Pages 1–14 1ki1 Evolutionary trace report by report maker June 20, 2010 4 Notes on using trace results 12 4.1 Coverage 12 4.2 Known substitutions 12 4.3 Surface 12 4.4 Number of contacts 12 4.5 Annotation 12 4.6 Mutation suggestions 12 5 Appendix 12 5.1 File formats 12 5.2 Color schemes used 12 5.3 Credits 12 5.3.1 Alistat 12 5.3.2 CE 13 5.3.3 DSSP 13 5.3.4 HSSP 13 5.3.5 LaTex 13 5.3.6 Muscle 13 5.3.7 Pymol 13 5.4 Note about ET Viewer 13 5.5 Citing this work 13 5.6 About report maker 13 CONTENTS 5.7 Attachments 13 1 Introduction 1 1 INTRODUCTION 2 Chain 1ki1A 1 From the original Protein Data Bank entry (PDB id 1ki1): 2.1 Q9DDV6 overview 1 Title: Guanine nucleotide exchange region of intersectin in complex 2.2 Multiple sequence alignment for 1ki1A 1 with cdc42 2.3 Residue ranking in 1ki1A 1 Compound: Mol id: 1; molecule: g25k gtp-binding protein, placen- 2.4 Top ranking residues in 1ki1A and their position on tal isoform; chain: a, c; fragment: residues 1-188; synonym: cdc42; the structure 2 engineered: yes; mutation: yes; mol id: 2; molecule: intersectin long 2.4.1 Clustering of residues at 25% coverage. 2 form; chain: b, d; fragment: dbl homology and pleckstrin homology 2.4.2 Overlap with known functional surfaces at domains (residues 1229-1580); engineered: yes 25% coverage. 2 Organism, scientific name: Homo Sapiens; 2.4.3 Possible novel functional surfaces at 25% 1ki1 contains unique chains 1ki1A (178 residues) and 1ki1B coverage. 4 (342 residues) 1ki1C is a homologue of chain 1ki1A. 1ki1D is a homologue of chain 1ki1B. 3 Chain 1ki1B 6 3.1 Q15811 overview 6 2 CHAIN 1KI1A 3.2 Multiple sequence alignment for 1ki1B 6 3.3 Residue ranking in 1ki1B 7 2.1 Q9DDV6 overview 3.4 Top ranking residues in 1ki1B and their position on From SwissProt, id Q9DDV6, 100% identical to 1ki1A: the structure 7 Description: Rho GTPase Cdc42 (MGC52619 protein) (Rho family 3.4.1 Clustering of residues at 25% coverage. 7 small GTP binding protein cdc42). 3.4.2 Overlap with known functional surfaces at Organism, scientific name: Xenopus laevis (African clawed frog). 25% coverage. 8 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 3.4.3 Possible novel functional surfaces at 25% Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoi- coverage. 10 dea; Pipidae; Xenopodinae; Xenopus; Xenopus. 1 Lichtarge lab 2006 Fig. 1. Residues 1-178 in 1ki1A colored by their relative importance. (See Appendix, Fig.15, for the coloring scheme.) 2.2 Multiple sequence alignment for 1ki1A For the chain 1ki1A, the alignment 1ki1A.msf (attached) with 505 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1ki1A.msf. Its statistics, from the alistat program are the following: Fig. 2. Residues in 1ki1A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 505 Total number of residues: 87877 Smallest: 136 belong to. The clusters in Fig.3 are composed of the residues listed Largest: 178 Average length: 174.0 Alignment length: 178 Average identity: 56% Most related pair: 99% Most unrelated pair: 22% Most distant seq: 47% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 50% eukaryotic ( 13% vertebrata, 1% arthropoda, 14% fungi, 9% plantae) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1ki1A.descr. 2.3 Residue ranking in 1ki1A The 1ki1A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1ki1A can be found in the file called 1ki1A.ranks sorted in the attachment. 2.4 Top ranking residues in 1ki1A and their position on the structure Fig. 3. Residues in 1ki1A, colored according to the cluster they belong to: In the following we consider residues ranking among top 25% of resi- red, followed by blue and yellow are the largest clusters (see Appendix for dues in the protein . Figure 2 shows residues in 1ki1A colored by their the coloring scheme). Clockwise: front, back, top and bottom views. The importance: bright red and yellow indicate more conserved/important corresponding Pymol script is attached. residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. in Table 1. 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 2 Table 1. Table 3. continued cluster size member res type disruptive color residues mutations red 44 5,10,11,12,14,15,16,17,28,29 12 G (R)(K)(EH)(FQW) 32,34,35,36,37,39,40,55,57 14 V (R)(KYE)(H)(Q) 58,59,60,61,62,64,67,68,70 62 E (H)(FW)(Y)(R) 71,72,82,89,92,97,100,114 17 T (K)(R)(FQMWH)(E) 116,118,120,154,156,157,158 169 Table 3. List of disruptive mutations for the top 25% of residues in 1ki1A, that are at the interface with sulfate ion. Table 1. Clusters of top ranking residues in 1ki1A. 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. Sulfate ion binding site. Table 2 lists the top 25% of residues at the interface with 1ki1SO44001 (sulfate ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 4.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 59 A A(99)S 0.02 4/1 3.78 15 G G(98)E. 0.07 15/15 2.76 16 K K(98).E 0.09 27/12 2.78 11 D D(97)N 0.16 4/4 3.64 .(1)EA 12 G G(97)A 0.16 9/9 3.63 .(1)SET MY 14 V V(67) 0.20 14/12 3.30 C(30)A .(1)I 62 E E(94) 0.23 2/0 4.27 Fig. 4. Residues in 1ki1A, at the interface with sulfate ion, colored by their D(3).AS relative importance. The ligand (sulfate ion) is colored green. Atoms further KF than 30A˚ away from the geometric center of the ligand, as well as on the line 17 T T(96)V 0.25 11/6 3.02 of sight to the ligand were removed. (See Appendix for the coloring scheme .(1) for the protein chain 1ki1A.) S(1)R Figure 4 shows residues in 1ki1A colored by their importance, at the Table 2. The top 25% of residues in 1ki1A at the interface with sulfate interface with 1ki1SO44001. 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 Interface with 1ki1D.By analogy with 1ki1C – 1ki1D interface. type in the bracket; noc/bb: number of contacts with the ligand, with the num- Table 4 lists the top 25% of residues at the interface with 1ki1D. The ber of contacts realized through backbone atoms given in the bracket; dist: following table (Table 5) suggests possible disruptive replacements distance of closest apporach to the ligand. ) for these residues (see Section 4.6). Table 4. Table 3. res type subst’s cvg noc/ dist A˚ res type disruptive (%) bb ( ) mutations 60 G G(99)SX 0.01 23/23 3.46 59 A (KR)(YE)(QH)(D) 59 A A(99)S 0.02 13/12 3.82 15 G (R)(K)(FWH)(M) 57 D D(99)CN 0.03 8/6 3.67 16 K (Y)(FW)(T)(VCAG) 34 P P(98)GS 0.05 15/10 2.98 11 D (R)(H)(FW)(Y) .QL continued in next column continued in next column 3 Table 4. continued Table 5. continued res type subst’s cvg noc/ dist res type disruptive (%) bb (A˚ ) mutations 37 F F(98) 0.06 10/10 3.01 61 Q (Y)(H)(FW)(T) L(1)A 35 T (R)(K)(H)(FW) 61 Q Q(98)PA 0.07 24/6 3.49 70 L (Y)(R)(T)(H) NMSKE 67 L (R)(Y)(H)(T) 35 T T(97) 0.12 53/14 2.74 64 Y (K)(Q)(R)(EM) S(1)I.P 71 S (R)(K)(H)(FQW) DN 32 Y (K)(M)(Q)(ER) 70 L L(96)M 0.14 33/9 3.02 36 V (Y)(R)(E)(K) F(1)RIV 40 Y (K)(QM)(E)(R) S 5 K (Y)(FW)(T)(CG) 67 L L(96) 0.15 48/10 3.24 39 N (Y)(FW)(H)(T) I(1)MFV S Table 5. List of disruptive mutations for the top 25% of residues in 1ki1A, 64 Y Y(92) 0.17 62/10 3.35 that are at the interface with 1ki1D. F(5).LS V 71 S S(90)G 0.18 14/8 3.58 A(3) C(4)NFE T 32 Y Y(96)H 0.20 104/8 2.13 .(1)INS 36 V V(93) 0.21 35/9 3.63 A(3).QP I(1)G 40 Y F(21) 0.21 10/10 3.83 Y(74) H(1)LRT QD 5 K K(95)Q 0.22 1/0 4.57 .(3)RS 39 N N(91) 0.24 37/8 3.07 K(1) D(1) H(1)Q T(1)VSR Table 4.
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