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1Civ Lichtarge Lab 2006 Pages 1–8 1civ Evolutionary trace report by report maker August 2, 2010 4.3.1 Alistat 7 4.3.2 CE 8 4.3.3 DSSP 8 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1civ): Title: Chloroplast nadp-dependent malate dehydrogenase from fla- veria bidentis Compound: Mol id: 1; molecule: nadp-malate dehydrogenase; CONTENTS chain: a; ec: 1.1.1.82 Organism, scientific name: Flaveria Bidentis; 1 Introduction 1 1civ contains a single unique chain 1civA (374 residues long). 2 Chain 1civA 1 2.1 Q42737 overview 1 2.2 Multiple sequence alignment for 1civA 1 2.3 Residue ranking in 1civA 1 2 CHAIN 1CIVA 2.4 Top ranking residues in 1civA and their position on the structure 1 2.1 Q42737 overview 2.4.1 Clustering of residues at 25% coverage. 2 From SwissProt, id Q42737, 100% identical to 1civA: 2.4.2 Overlap with known functional surfaces at Description: NADP-malate dehydrogenase. 25% coverage. 2 Organism, scientific name: Flaveria trinervia (Clustered yellow- 2.4.3 Possible novel functional surfaces at 25% tops). coverage. 4 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3 Notes on using trace results 6 eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Aste- 3.1 Coverage 6 roideae; Tageteae; Flaveria. 3.2 Known substitutions 6 3.3 Surface 7 3.4 Number of contacts 7 3.5 Annotation 7 2.2 Multiple sequence alignment for 1civA 3.6 Mutation suggestions 7 For the chain 1civA, the alignment 1civA.msf (attached) with 308 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 7 database, and fragments shorter than 75% of the query as well as 4.1 File formats 7 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 7 to this report, under the name of 1civA.msf. Its statistics, from the 4.3 Credits 7 alistat program are the following: 1 Lichtarge lab 2006 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. 1. Residues 12-198 in 1civA colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 2. Residues 199-385 in 1civA colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Fig. 3. Residues in 1civA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 308 Total number of residues: 100746 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 284 top 25% of all residues, this time colored according to clusters they Largest: 374 belong to. The clusters in Fig.4 are composed of the residues listed Average length: 327.1 in Table 1. Alignment length: 374 Average identity: 50% Table 1. Most related pair: 99% cluster size member Most unrelated pair: 24% color residues Most distant seq: 38% red 72 49,52,54,56,58,116,124,126 133,134,135,136,138,139,140 143,146,147,150,151,154,158 Furthermore, <1% of residues show as conserved in this ali- 166,167,168,169,170,171,172 gnment. 173,174,175,182,189,190,193 The alignment consists of 29% eukaryotic ( 4% vertebrata, <1% 195,196,197,199,200,201,222 arthropoda, 14% plantae), and 10% prokaryotic sequences. (Des- 223,224,225,226,229,231,232 criptions of some sequences were not readily available.) The file 257,261,264,265,268,269,272 containing the sequence descriptions can be found in the attachment, 273,275,276,277,279,280,281 under the name 1civA.descr. 283,302,312,321,323,354,355 2.3 Residue ranking in 1civA 358 blue 11 76,78,88,90,93,94,95,97,99 The 1civA sequence is shown in Figs. 1–2, with each residue colored 101,103 according to its estimated importance. The full listing of residues yellow 3 63,65,69 in 1civA can be found in the file called 1civA.ranks sorted in the green 2 291,330 attachment. purple 2 129,130 2.4 Top ranking residues in 1civA and their position on azure 2 294,295 the structure continued in next column In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 3 shows residues in 1civA colored by their 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) VS 272 W R(85) 0.07 1/1 4.77 W(13)S. 99 L A(83) 0.11 70/24 3.55 L(13) C(1). S(1)T 275 S S(94)YA 0.11 4/4 3.90 PT(3)G 95 L L(92) 0.13 2/2 4.79 I(5).M 93 M M(92) 0.16 44/10 3.32 A(2)Y. L(2)FI 88 L L(84) 0.17 2/2 4.53 V(5) A(7) M(1).QC 101 P P(95)GR 0.17 5/5 4.49 Fig. 4. Residues in 1civA, colored according to the cluster they belong to: TE.DLAQ red, followed by blue and yellow are the largest clusters (see Appendix for 103 L L(92) 0.19 12/9 3.29 the coloring scheme). Clockwise: front, back, top and bottom views. The V(5)IF. corresponding Pymol script is attached. C 268 L I(59) 0.20 28/4 3.45 L(13) Table 1. continued V(27). cluster size member 52 G G(93) 0.21 1/1 5.00 color residues .(5)V 206 A A(85) 0.22 4/2 3.71 Table 1. Clusters of top ranking residues in 1civA. S(13)GL 56 N Y(80) 0.23 26/6 3.13 N(13) 2.4.2 Overlap with known functional surfaces at 25% coverage. .(4) The name of the ligand is composed of the source PDB identifier S(1) and the heteroatom name used in that file. 91 V T(4) 0.25 10/6 3.40 Interface with 1civA1.Table 2 lists the top 25% of residues at V(82) the interface with 1civA1. The following table (Table 3) suggests L(7) possible disruptive replacements for these residues (see Section 3.6). I(2) Table 2. C(2). res type subst’s cvg noc/ dist 278 A A(69) 0.25 26/14 3.49 (%) bb (A˚ ) L(13)I 264 R R(99). 0.02 54/1 2.72 M(13) 97 D D(99). 0.03 63/14 2.72 G(1)FVS 200 R R(99)K 0.03 22/10 3.77 94 E E(99)Q. 0.04 61/11 2.70 Table 2. The top 25% of residues in 1civA at the interface with 1civA1. 279 S S(99)EC 0.04 28/8 2.70 (Field names: res: residue number in the PDB entry; type: amino acid type; 90 G G(94) 0.06 13/13 3.45 substs: substitutions seen in the alignment; with the percentage of each type A(5). in the bracket; noc/bb: number of contacts with the ligand, with the number of 199 N N(98)LD 0.06 28/15 3.52 contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 276 S S(98)AR 0.06 9/7 3.25 P 277 A A(96)ET 0.06 4/4 3.85 continued in next column 3 Table 3. Figure 5 shows residues in 1civA colored by their importance, at the res type disruptive interface with 1civA1. mutations NAP binding site. Table 4 lists the top 25% of residues at the inter- 264 R (TD)(SVCLAPIG)(YE)(FMW) face with 1civNAP386 (nap). The following table (Table 5) suggests 97 D (R)(FWH)(VCAG)(KY) possible disruptive replacements for these residues (see Section 3.6). 200 R (T)(YD)(SVCAG)(FELWPI) 94 E (FWH)(YVCAG)(TR)(S) Table 4. 279 S (R)(K)(FWH)(Q) res type subst’s cvg noc/ dist 90 G (KER)(HD)(Q)(FMW) (%) bb (A˚ ) 199 N (Y)(H)(FW)(TR) 143 N N(99)H 0.02 1/0 4.51 276 S (KR)(YH)(FEQW)(M) 196 L L(99)I 0.02 6/0 3.88 277 A (R)(K)(Y)(H) 197 D D(99)E 0.02 1/0 4.79 272 W (E)(K)(D)(TQ) 169 N N(99)GD 0.04 54/18 2.69 99 L (R)(Y)(H)(K) M 275 S (KR)(Q)(H)(M) 146 I I(98)LV 0.05 14/0 3.85 95 L (Y)(R)(TH)(SCG) 276 S S(98)AR 0.06 1/0 4.90 93 M (Y)(T)(HR)(CG) P 88 L (Y)(R)(H)(T) 126 G G(92) 0.07 31/31 3.85 101 P (Y)(R)(H)(T) A(5)SDC 103 L (R)(Y)(H)(T) 225 H AH(99)P 0.07 21/0 2.90 268 L (YR)(H)(T)(KE) R 52 G (KER)(HD)(Q)(FMW) 168 G G(84) 0.08 15/15 3.24 206 A (R)(K)(YE)(H) A(15) 56 N (FYWH)(R)(TEVA)(MCG) 280 T A(81) 0.09 9/0 3.65 91 V (R)(K)(E)(Y) T(13) 278 A (R)(KY)(E)(H) P(3)GN 275 S S(94)YA 0.11 2/0 4.68 Table 3.
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