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1Ezw Lichtarge Lab 2006 Pages 1–8 1ezw Evolutionary trace report by report maker March 17, 2010 4.3.1 Alistat 8 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 1ezw): Title: Structure of coenzyme f420 dependent tetrahydromethanopte- rin reductase from methanopyrus kandleri Compound: Mol id: 1; molecule: coenzyme f420-dependent n5,n10- methylenetetrahydromethanopterin reductase; chain: a Organism, scientific name: Methanopyrus Kandleri; 1ezw contains a single unique chain 1ezwA (347 residues long). CONTENTS 2 CHAIN 1EZWA 2.1 Q8TXY4 overview 1 Introduction 1 From SwissProt, id Q8TXY4, 99% identical to 1ezwA: 2 Chain 1ezwA 1 Description: 5,10-methylenetetrahydromethanopterin reductase 2.1 Q8TXY4 overview 1 (EC 1.5.99.11) (Coenzyme F420-dependent N(5),N(10)- 2.2 Multiple sequence alignment for 1ezwA 1 methylenetetrahydromethanopterin reductase) (Methylene-H(4)MPT 2.3 Residue ranking in 1ezwA 1 reductase). 2.4 Top ranking residues in 1ezwA and their position on Organism, scientific name: Methanopyrus kandleri. the structure 1 Taxonomy: Archaea; Euryarchaeota; Methanopyri; Methanopyrales; 2.4.1 Clustering of residues at 25% coverage. 2 Methanopyraceae; Methanopyrus. 2.4.2 Overlap with known functional surfaces at Function: Catalyzes the reversible reduction of methylene-H(4)MPT 25% coverage. 2 to methyl-H(4)MPT. 2.4.3 Possible novel functional surfaces at 25% Catalytic activity: 5-methyltetrahydromethanopterin + coenzyme coverage. 5 F420 = 5,10-methylenetetrahydromethanopterin + reduced coen- zyme F420. 3 Notes on using trace results 6 Enzyme regulation: Requires the presence of relatively high con- 3.1 Coverage 6 centrations of either sulfate or phosphate for maximal activity. 3.2 Known substitutions 7 Pathway: Methanogenesis from carbon dioxide; fifth step. 3.3 Surface 7 Subunit: Homotetramer composed of two loosely associated dimers 3.4 Number of contacts 7 (Probable). 3.5 Annotation 7 Subcellular location: Cytoplasmic. 3.6 Mutation suggestions 7 Similarity: Belongs to the mer family. About: This Swiss-Prot entry is copyright. It is produced through a 4 Appendix 7 collaboration between the Swiss Institute of Bioinformatics and the 4.1 File formats 7 EMBL outstation - the European Bioinformatics Institute. There are 4.2 Color schemes used 7 no restrictions on its use as long as its content is in no way modified 4.3 Credits 8 and this statement is not removed. 1 Lichtarge lab 2006 in 1ezwA can be found in the file called 1ezwA.ranks sorted in the attachment. 2.4 Top ranking residues in 1ezwA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1ezwA 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. Fig. 1. Residues 2-174 in 1ezwA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 2. Residues 175-348 in 1ezwA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) 2.2 Multiple sequence alignment for 1ezwA For the chain 1ezwA, the alignment 1ezwA.msf (attached) with 33 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 1ezwA.msf. Its statistics, from the Fig. 3. Residues in 1ezwA, colored by their relative importance. Clockwise: alistat program are the following: front, back, top and bottom views. Format: MSF Number of sequences: 33 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 10589 top 25% of all residues, this time colored according to clusters they Smallest: 288 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 347 in Table 1. Average length: 320.9 Alignment length: 347 Table 1. Average identity: 45% cluster size member Most related pair: 98% color residues Most unrelated pair: 19% red 82 7,8,9,10,12,26,27,30,35,39 Most distant seq: 31% 40,42,49,53,56,62,64,65,67 69,85,87,89,90,91,94,96,97 98,99,127,172,174,176,177 Furthermore, 3% of residues show as conserved in this alignment. 178,179,180,182,186,187,191 The alignment consists of 9% prokaryotic, and 30% archaean 192,194,196,197,198,200,202 sequences. (Descriptions of some sequences were not readily availa- 206,210,213,228,229,233,241 ble.) The file containing the sequence descriptions can be found in 244,245,248,249,250,251,252 the attachment, under the name 1ezwA.descr. 255,257,263,264,281,283,290 continued in next column 2.3 Residue ranking in 1ezwA The 1ezwA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues 2 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 56 T (KR)(FQMWH)(NELPI)(D) 90 R (TD)(SYEVCLAPIG)(FMW)(N) 53 A (YR)(K)(H)(E) Table 3. List of disruptive mutations for the top 25% of residues in 1ezwA, that are at the interface with magnesium ion. Fig. 4. Residues in 1ezwA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 1. continued cluster size member color residues 298,302,304,314,318,319,325 326,327,329,336,338 blue 3 73,77,78 Table 1. Clusters of top ranking residues in 1ezwA. Fig. 5. Residues in 1ezwA, at the interface with magnesium ion, colored 2.4.2 Overlap with known functional surfaces at 25% coverage. by their relative importance. The ligand (magnesium ion) is colored green. The name of the ligand is composed of the source PDB identifier Atoms further than 30A˚ away from the geometric center of the ligand, as well and the heteroatom name used in that file. as on the line of sight to the ligand were removed. (See Appendix for the Magnesium ion binding site. Table 2 lists the top 25% of residues coloring scheme for the protein chain 1ezwA.) at the interface with 1ezwAMG361 (magnesium ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Figure 5 shows residues in 1ezwA colored by their importance, at the interface with 1ezwAMG361. Table 2. Interface with 1ezwA1.Table 4 lists the top 25% of residues at res type subst’s cvg noc/ dist the interface with 1ezwA1. The following table (Table 5) suggests (%) bb (A˚ ) possible disruptive replacements for these residues (see Section 3.6). 56 T T(100) 0.04 4/4 2.27 Table 4. 90 R R(100) 0.04 2/0 3.95 res type subst’s cvg noc/ dist 53 A A(93) 0.10 2/2 3.58 (%) bb (A˚ ) M(3) 27 E E(100) 0.04 2/0 4.08 S(3) 56 T T(100) 0.04 4/4 3.67 89 G G(100) 0.04 2/2 4.87 Table 2. The top 25% of residues in 1ezwA at the interface with magne- 90 R R(100) 0.04 9/0 3.00 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 continued in next column each type in the bracket; noc/bb: number of contacts with the ligand, with 3 Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) 53 A A(93) 0.10 3/3 4.42 M(3) S(3) 87 S S(90) 0.11 6/6 3.21 A(6) T(3) 85 W E(81) 0.16 35/6 2.93 T(3) A(6) L(3) W(3) H(3) Table 4. The top 25% of residues in 1ezwA at the interface with 1ezwA1. (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. ) Fig. 6. Residues in 1ezwA, at the interface with 1ezwA1, colored by their relative importance. 1ezwA1 is shown in backbone representation (See Table 5. Appendix for the coloring scheme for the protein chain 1ezwA.) res type disruptive mutations 27 E (FWH)(YVCARG)(T)(SNKLPI) Table 6. continued 56 T (KR)(FQMWH)(NELPI)(D) res type subst’s cvg noc/ dist 89 G (KER)(FQMWHD)(NYLPI)(SVA) A˚ 90 R (TD)(SYEVCLAPIG)(FMW)(N) (%) bb ( ) 53 A (YR)(K)(H)(E) Y(3) 87 S (KR)(QH)(FMW)(E) D(6) 85 W (K)(E)(Q)(R) L(3) M(3) 78 S S(84) 0.14 42/13 2.77 Table 5. List of disruptive mutations for the top 25% of residues in M(3) 1ezwA, that are at the interface with 1ezwA1.
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