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1Ytm Lichtarge Lab 2006 Pages 1–8 1ytm Evolutionary trace report by report maker April 11, 2010 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 7 4.4 Note about ET Viewer 7 4.5 Citing this work 7 4.6 About report maker 8 4.7 Attachments 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ytm): Title: Crystal structure of phosphoenolpyruvate carboxykinase of anaerobiospirillum succiniciproducens complexed with atp, oxalate, magnesium and manganese ions Compound: Mol id: 1; molecule: phosphoenolpyruvate carboxy- kinase [atp]; chain: a, b; synonym: pep carboxykinase; phosphoe- nolpyruvate carboxylase; pepck; ec: 4.1.1.49; engineered: yes Organism, scientific name: Anaerobiospirillum Succiniciprodu- cens; 1ytm contains a single unique chain 1ytmA (517 residues long) CONTENTS and its homologue 1ytmB. 1 Introduction 1 2 CHAIN 1YTMA 2.1 O09460 overview 2 Chain 1ytmA 1 2.1 O09460 overview 1 From SwissProt, id O09460, 97% identical to 1ytmA: 2.2 Multiple sequence alignment for 1ytmA 1 Description: Phosphoenolpyruvate carboxykinase [ATP] (EC 2.3 Residue ranking in 1ytmA 1 4.1.1.49) (PEP carboxykinase) (Phosphoenolpyruvate carboxylase) 2.4 Top ranking residues in 1ytmA and their position on (PEPCK). the structure 1 Organism, scientific name: Anaerobiospirillum succiniciprodu- 2.4.1 Clustering of residues at 25% coverage. 2 cens. 2.4.2 Overlap with known functional surfaces at Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Aero- 25% coverage. 3 monadales; Succinivibrionaceae; Anaerobiospirillum. Catalytic activity: ATP + oxaloacetate = ADP + phosphoenolpyru- 3 Notes on using trace results 6 vate + CO(2). 3.1 Coverage 6 Pathway: Rate-limiting gluconeogenic enzyme. 3.2 Known substitutions 6 Subcellular location: Cytoplasmic (By similarity). 3.3 Surface 6 Similarity: Belongs to the phosphoenolpyruvate carboxykinase 3.4 Number of contacts 6 [ATP] family. 3.5 Annotation 6 About: This Swiss-Prot entry is copyright. It is produced through a 3.6 Mutation suggestions 6 collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are 4 Appendix 6 no restrictions on its use as long as its content is in no way modified 4.1 File formats 6 and this statement is not removed. 4.2 Color schemes used 7 4.3 Credits 7 2.2 Multiple sequence alignment for 1ytmA 4.3.1 Alistat 7 For the chain 1ytmA, the alignment 1ytmA.msf (attached) with 396 4.3.2 CE 7 sequences was used. The alignment was downloaded from the HSSP 1 Lichtarge lab 2006 Fig. 1. Residues 2-259 in 1ytmA colored by their relative importance. (See Fig. 2. Residues 260-518 in 1ytmA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) Appendix, Fig.9, for the coloring scheme.) 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 1ytmA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 396 Total number of residues: 198506 Smallest: 403 Largest: 517 Average length: 501.3 Alignment length: 517 Average identity: 49% Most related pair: 99% Most unrelated pair: 24% Most distant seq: 52% Furthermore, 3% of residues show as conserved in this alignment. The alignment consists of 7% eukaryotic ( 3% fungi, 2% plan- tae), and 9% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descrip- Fig. 3. Residues in 1ytmA, colored by their relative importance. Clockwise: tions can be found in the attachment, under the name 1ytmA.descr. front, back, top and bottom views. 2.3 Residue ranking in 1ytmA 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the The 1ytmA sequence is shown in Figs. 1–2, with each residue colored top 25% of all residues, this time colored according to clusters they according to its estimated importance. The full listing of residues belong to. The clusters in Fig.4 are composed of the residues listed in 1ytmA can be found in the file called 1ytmA.ranks sorted in the in Table 1. attachment. Table 1. cluster size member 2.4 Top ranking residues in 1ytmA and their position on color residues the structure red 122 54,55,58,59,60,61,62,64,65 In the following we consider residues ranking among top 25% of 119,135,136,139,140,145,200 residues in the protein . Figure 3 shows residues in 1ytmA colored 201,202,203,205,206,209,213 by their importance: bright red and yellow indicate more conser- 214,217,224,225,226,227,229 ved/important residues (see Appendix for the coloring scheme). A continued in next column Pymol script for producing this figure can be found in the attachment. 2 Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 248 K K(100) 0.04 2/0 4.97 249 T T(100) 0.04 5/2 2.11 262 D D(99)N 0.06 5/2 3.76 263 D D(99)E 0.06 3/0 4.31 327 R R(99)Y 0.06 1/0 4.33 280 Y Y(98)T. 0.09 2/2 4.19 281 A A(98)I. 0.09 1/1 4.92 Table 2. The top 25% of residues in 1ytmA at the interface with magne- sium 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 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 248 K (Y)(FTW)(SVCAG)(HD) Fig. 4. Residues in 1ytmA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for 249 T (KR)(FQMWH)(NELPI)(D) the coloring scheme). Clockwise: front, back, top and bottom views. The 262 D (R)(FWH)(Y)(VCAG) corresponding Pymol script is attached. 263 D (R)(FWH)(YVCAG)(K) 327 R (D)(TEVLAPI)(SMCG)(FNYW) 280 Y (K)(M)(Q)(LPI) Table 1. continued 281 A (Y)(R)(KE)(H) cluster size member color residues Table 3. List of disruptive mutations for the top 25% of residues in 240,241,242,243,244,245,246 1ytmA, that are at the interface with magnesium ion. 247,248,249,250,251,252,254 257,259,260,261,262,263,264 Figure 5 shows residues in 1ytmA colored by their importance, at the 265,266,267,273,274,276,277 interface with 1ytmMG998. 278,279,280,281,282,286,291 Oxalic acid binding site. Table 4 lists the top 25% of residues 292,294,297,305,306,323,325 at the interface with 1ytmOXD543 (oxalic acid). The following table 327,330,331,335,348,354,357 (Table 5) suggests possible disruptive replacements for these residues 358,360,361,363,364,368,372 (see Section 3.6). 375,376,377,379,380,381,382 387,388,389,391,399,400,402 Table 4. 403,404,406,407,412,415,416 res type subst’s cvg noc/ dist 419,432,434,435,436,437,439 (%) bb (A˚ ) 441,443,449,450,490,507,511 206 K K(100) 0.04 15/0 3.33 514 244 S S(100) 0.04 13/5 2.32 205 K K(99)N 0.06 2/0 4.24 Table 1. Clusters of top ranking residues in 1ytmA. 263 D D(99)E 0.06 9/0 3.48 327 R R(99)Y 0.06 12/0 3.46 200 Y Y(99)F 0.07 5/0 3.66 2.4.2 Overlap with known functional surfaces at 25% coverage. 280 Y Y(98)T. 0.09 7/1 3.81 The name of the ligand is composed of the source PDB identifier 407 F F(99)L 0.09 9/0 3.45 and the heteroatom name used in that file. 60 R R(99).H 0.12 16/0 2.76 Magnesium ion binding site. Table 2 lists the top 25% of residues 225 H H(97) 0.14 8/0 3.46 at the interface with 1ytmMG998 (magnesium ion). The following L(1)Y table (Table 3) suggests possible disruptive replacements for these 388 T T(96) 0.18 2/1 4.35 residues (see Section 3.6). V(2)L.I continued in next column 3 Table 5. continued res type disruptive mutations Table 5. List of disruptive mutations for the top 25% of residues in 1ytmA, that are at the interface with oxalic acid. Fig. 5. Residues in 1ytmA, at the interface with magnesium ion, colored by their relative importance. The ligand (magnesium ion) 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 chain 1ytmA.) Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) Fig. 6. Residues in 1ytmA, at the interface with oxalic acid, colored by their S relative importance. The ligand (oxalic acid) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line Table 4. The top 25% of residues in 1ytmA at the interface with oxalic of sight to the ligand were removed. (See Appendix for the coloring scheme acid.(Field names: res: residue number in the PDB entry; type: amino acid for the protein chain 1ytmA.) 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- ber of contacts realized through backbone atoms given in the bracket; dist: Figure 6 shows residues in 1ytmA colored by their importance, at the distance of closest apporach to the ligand.
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