Pages 1–8 1z8d Evolutionary trace report by report maker October 30, 2009 4.3.1 Alistat 7 4.3.2 CE 7 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 1z8d): Title: Crystal structure of human muscle glycogen phosphorylase a with amp and glucose Compound: Mol id: 1; molecule: glycogen phosphorylase, muscle form; chain: a; synonym: myophosphorylase; ec: 2.4.1.1; enginee- red: yes; mutation: yes Organism, scientific name: Homo Sapiens; 1z8d contains a single unique chain 1z8dA (821 residues long). CONTENTS 1 Introduction 1 2 CHAIN 1Z8DA 2.1 P11217 overview 2 Chain 1z8dA 1 2.1 P11217 overview 1 From SwissProt, id P11217, 95% identical to 1z8dA: 2.2 Multiple sequence alignment for 1z8dA 1 Description: Glycogen phosphorylase, muscle form (EC 2.4.1.1) 2.3 Residue ranking in 1z8dA 1 (Myophosphorylase). 2.4 Top ranking residues in 1z8dA and their position on Organism, scientific name: Homo sapiens (Human). the structure 2 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 2.4.1 Clustering of residues at 25% coverage. 2 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; 2.4.2 Overlap with known functional surfaces at Catarrhini; Hominidae; Homo. 25% coverage. 3 Function: Phosphorylase is an important allosteric enzyme in carbo- 2.4.3 Possible novel functional surfaces at 25% hydrate metabolism. Enzymes from different sources differ in their coverage. 5 regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties. 3 Notes on using trace results 6 Catalytic activity: (1,4-alpha-D-glucosyl)(n) + phosphate = (1,4- 3.1 Coverage 6 alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate. 3.2 Known substitutions 6 Cofactor: Pyridoxal phosphate. 3.3 Surface 6 Enzyme regulation: Activity of phosphorylase is controlled both 3.4 Number of contacts 7 by allosteric means (through the noncovalent binding of metaboli- 3.5 Annotation 7 tes) and by covalent modification. Thus AMP allosterically activates, 3.6 Mutation suggestions 7 whereas ATP, ADP, and glucose-6-phosphate allosterically inhibit, phosphorylase B. 4 Appendix 7 Subunit: Homodimer. Dimers associate into a tetramer to form the 4.1 File formats 7 enzymatically active phosphorylase A. 4.2 Color schemes used 7 Ptm: Phosphorylation of Ser-14 converts phosphorylase B (unphos- 4.3 Credits 7 phorylated) to phosphorylase A. 1 Lichtarge lab 2006 Disease: Defects in PYGM are the cause of glycogen storage disease V (GSD-V) [MIM:232600]; also known as McArdle’s disease. GSD- V is a form of autosomal recessive myopathy characterized by exercise intolerance, muscle cramps, and recurrent myoglobinuria. Similarity: Belongs to the glycogen phosphorylase family. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Multiple sequence alignment for 1z8dA For the chain 1z8dA, the alignment 1z8dA.msf (attached) with 516 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 1z8dA.msf. Its statistics, from the Fig. 1. Residues 2-288 in 1z8dA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) alistat program are the following: Format: MSF Number of sequences: 516 Total number of residues: 404536 Smallest: 715 Largest: 821 Average length: 784.0 Alignment length: 821 Average identity: 46% Most related pair: 99% Most unrelated pair: 26% Most distant seq: 46% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 9% eukaryotic ( 2% vertebrata, <1% arthropoda, 2% fungi, 2% plantae), and 12% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file Fig. 2. Residues 289-561 in 1z8dA colored by their relative importance. (See containing the sequence descriptions can be found in the attachment, Appendix, Fig.11, for the coloring scheme.) under the name 1z8dA.descr. 2.3 Residue ranking in 1z8dA The 1z8dA sequence is shown in Figs. 1–3, with each residue colored according to its estimated importance. The full listing of residues in 1z8dA can be found in the file called 1z8dA.ranks sorted in the attachment. 2.4 Top ranking residues in 1z8dA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 4 shows residues in 1z8dA 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. 5 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.5 are composed of the residues listed Fig. 3. Residues 562-836 in 1z8dA colored by their relative importance. (See in Table 1. Appendix, Fig.11, for the coloring scheme.) 2 Table 1. cluster size member color residues red 196 84,86,88,89,90,92,93,101,126 128,129,131,132,133,134,135 136,137,138,139,140,141,142 143,145,146,148,156,157,158 159,160,161,164,165,166,168 175,177,180,182,189,204,215 223,225,227,232,241,242,243 244,279,280,281,283,288,291 292,293,295,296,297,298,302 336,337,338,339,340,341,342 348,351,353,355,364,374,375 376,377,378,379,380,382,383 384,385,387,396,397,398,441 442,444,453,454,455,456,459 462,468,471,476,479,481,482 483,484,485,487,489,490,491 496,499,538,542,563,564,566 568,569,571,572,573,574,575 576,578,579,601,607,608,609 Fig. 4. Residues in 1z8dA, colored by their relative importance. Clockwise: 610,611,612,613,616,617,620 front, back, top and bottom views. 644,647,648,650,653,654,658 659,661,663,664,665,666,667 668,669,670,672,673,674,675 676,677,678,679,680,681,684 685,686,688,690,691,693,694 695,696,698,699,711,712,769 771,776,780,797,811,812,813 814,815,820,824,825 blue 3 704,707,804 yellow 3 587,631,633 green 2 406,407 Table 1. Clusters of top ranking residues in 1z8dA. 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. Glucose binding site. Table 2 lists the top 25% of residues at the interface with 1z8dGLC901 (glucose). 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 Fig. 5. Residues in 1z8dA, colored according to the cluster they belong to: (%) bb (A˚ ) red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The 377 H H(100) 0.01 37/14 2.70 corresponding Pymol script is attached. 484 N N(99)A 0.02 10/0 2.87 672 E E(99)Q 0.02 14/3 2.69 674 S S(99)G 0.02 20/14 3.14 675 G G(99)D 0.02 12/12 2.75 136 L L(99)G. 0.04 17/11 3.37 139 L L(99)Q. 0.04 8/0 3.48 continued in next column 3 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) 676 T T(99)Q 0.04 5/1 4.08 680 X K(99)CX 0.04 1/0 4.95 135 G G(99)E. 0.06 15/15 3.72 D 574 K K(99).R 0.07 1/0 4.92 673 A A(99)G 0.07 11/6 3.62 455 V V(99).T 0.08 7/0 3.20 A 573 Y Y(99).C 0.08 5/0 3.12 S 283 D D(99)GA 0.11 1/0 4.67 SEN Table 2. The top 25% of residues in 1z8dA at the interface with glu- cose.(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- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Fig. 6. Residues in 1z8dA, at the interface with glucose, colored by their relative importance. The ligand (glucose) is colored green. Atoms further than Table 3. 30A˚ away from the geometric center of the ligand, as well as on the line of res type disruptive sight to the ligand were removed. (See Appendix for the coloring scheme for mutations the protein chain 1z8dA.) 377 H (E)(TQMD)(SNKVCLAPIG)(YR) 484 N (Y)(H)(FTEWR)(SCDG) 672 E (FWH)(Y)(VCAG)(TR) Table 4.