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2Ux8 Lichtarge Lab 2006 Pages 1–8 2ux8 Evolutionary trace report by report maker January 2, 2010 4.3.3 DSSP 7 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 2ux8): Title: Crystal structure of sphingomonas elodea atcc 31461 glucose- 1-phosphate uridylyltransferase in complex with glucose-1- phos- phate. Compound: Mol id: 1; molecule: glucose-1-phosphate uridylyl- transferase; chain: a, b, c, d, e, f, g, h; ec: 2.7.7.9; engineered: yes; CONTENTS other details: co-crystallised with glucose-1-phosphate Organism, scientific name: Sphingomonas Elodea; 1 Introduction 1 2ux8 contains a single unique chain 2ux8G (288 residues long) and its homologues 2ux8F, 2ux8A, 2ux8E, 2ux8B, 2ux8H, 2ux8C, 2 Chain 2ux8G 1 and 2ux8D. 2.1 Q8RTG2 overview 1 2.2 Multiple sequence alignment for 2ux8G 1 2.3 Residue ranking in 2ux8G 1 2.4 Top ranking residues in 2ux8G and their position on the structure 2 2 CHAIN 2UX8G 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Overlap with known functional surfaces at 2.1 Q8RTG2 overview 25% coverage. 2 From SwissProt, id Q8RTG2, 100% identical to 2ux8G: Description: UDP glucose pyrophosphorylase. 3 Notes on using trace results 6 Organism, scientific name: Pseudomonas paucimobilis (Sphingo- 3.1 Coverage 6 monas paucimobilis). 3.2 Known substitutions 6 Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Sphingo- 3.3 Surface 6 monadales; Sphingomonadaceae; Sphingomonas. 3.4 Number of contacts 7 3.5 Annotation 7 3.6 Mutation suggestions 7 2.2 Multiple sequence alignment for 2ux8G 4 Appendix 7 For the chain 2ux8G, the alignment 2ux8G.msf (attached) with 746 4.1 File formats 7 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 7 database, and fragments shorter than 75% of the query as well as 4.3 Credits 7 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 7 to this report, under the name of 2ux8G.msf. Its statistics, from the 4.3.2 CE 7 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 2-145 in 2ux8G colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 2. Residues 146-289 in 2ux8G colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Fig. 3. Residues in 2ux8G, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 746 Total number of residues: 204308 Smallest: 66 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 288 Average length: 273.9 Alignment length: 288 Average identity: 45% Most related pair: 99% Most unrelated pair: 0% Most distant seq: 35% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 23% prokaryotic, and 1% archaean 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 2ux8G.descr. 2.3 Residue ranking in 2ux8G The 2ux8G sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 2ux8G can be found in the file called 2ux8G.ranks sorted in the attachment. 2.4 Top ranking residues in 2ux8G and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 2ux8G, colored according to the cluster they belong to: residues in the protein . Figure 3 shows residues in 2ux8G colored red, followed by blue and yellow are the largest clusters (see Appendix for by their importance: bright red and yellow indicate more conser- the coloring scheme). Clockwise: front, back, top and bottom views. The ved/important residues (see Appendix for the coloring scheme). A corresponding Pymol script is attached. 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. 4 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 63 8,12,14,15,17,18,19,20,21,22 113 H (E)(M)(Q)(TD) 23,24,25,28,29,30,31,32,33 60 G (R)(K)(E)(FWH) 35,38,46,47,51,60,63,105,110 111,112,113,114,118,127,129 Table 3. List of disruptive mutations for the top 25% of residues in 131,132,133,134,171,172,191 2ux8G, that are at the interface with 2ux8H. 192,193,206,207,208,210,215 218,224,226,228,230,231,232 233,253,255,256,257,261,265 blue 3 76,77,80 yellow 2 198,200 Table 1. Clusters of top ranking residues in 2ux8G. 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. Interface with 2ux8H.Table 2 lists the top 25% of residues at the interface with 2ux8H. 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 (%) bb (A˚ ) 105 Q Q(99).P 0.02 6/6 3.76 E 70 F F(93)Y 0.11 2/2 4.41 L(2)T .(1)IWV RA 113 H H(82) 0.19 4/0 4.58 Fig. 5. Residues in 2ux8G, at the interface with 2ux8H, colored by their rela- D(15)ER tive importance. 2ux8H is shown in backbone representation (See Appendix N(1).YS for the coloring scheme for the protein chain 2ux8G.) TQG 60 G G(65) 0.24 2/2 4.79 A(2) Figure 5 shows residues in 2ux8G colored by their importance, at the S(11) interface with 2ux8H. H(14) G1P binding site. By analogy with 2ux8A – 2ux8AG1P1290 N(2)PD. interface. Table 4 lists the top 25% of residues at the interface ERT with 2ux8AG1P1290 (g1p). The following table (Table 5) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. The top 25% of residues in 2ux8G at the interface with 2ux8H. Table 4. (Field names: res: residue number in the PDB entry; type: amino acid type; res type subst’s cvg noc/ dist antn substs: substitutions seen in the alignment; with the percentage of each type (%) bb (A˚ ) in the bracket; noc/bb: number of contacts with the ligand, with the number of 192 K K(99)N. 0.01 2/0 3.66 contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 208 Y Y(98)FC 0.02 8/0 3.02 site .V 133 D D(99)SG 0.03 2/0 4.60 Table 3. res type disruptive 131 L L(95)A 0.04 14/0 3.20 mutations V(1)I 105 Q (Y)(H)(FTW)(CG) N(1)F 70 F (K)(E)(Q)(D) Y(1)TW. continued in next column continued in next column 3 Table 4. continued Table 5. continued res type subst’s cvg noc/ dist antn res type disruptive (%) bb (A˚ ) mutations 206 G G(98)SP 0.04 8/8 3.99 204 V (R)(Y)(K)(E) .A 255 D D(97) 0.04 2/0 4.63 Table 5. List of disruptive mutations for the top 25% of residues in .(1)NMR 2ux8G, that are at the interface with G1P. 111 L L(95) 0.06 8/1 3.97 site T(2)FN. IPYV 171 Y Y(91) 0.12 5/0 3.81 site V(2) S(2) F(2)HTA .IW 134 D D(65) 0.18 15/0 3.64 N(3) M(5) T(3) V(15) E(3)S I(1)HY. 253 R R(68) 0.20 1/0 4.59 W(5) T(7)I S(12) .(1)MNH LYACGV 204 V V(35) 0.25 10/8 2.82 I(49) N(1) A(8) L(2)TC Fig. 6. Residues in 2ux8G, at the interface with G1P, colored by their relative S(1)M. importance. The ligand (G1P) 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 Table 4. The top 25% of residues in 2ux8G at the interface with chain 2ux8G.) G1P.(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 num- Figure 6 shows residues in 2ux8G colored by their importance, at the ber of contacts realized through backbone atoms given in the bracket; dist: interface with 2ux8AG1P1290. distance of closest apporach to the ligand. ) G1P binding site. Table 6 lists the top 25% of residues at the interface with 2ux8GG1P1290 (g1p). The following table (Table Table 5. 7) suggests possible disruptive replacements for these residues (see Section 3.6). res type disruptive mutations Table 6.
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