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1W25 Lichtarge Lab 2006 Pages 1–12 1w25 Evolutionary trace report by report maker March 6, 2010 4.3.1 Alistat 10 4.3.2 CE 11 4.3.3 DSSP 11 4.3.4 HSSP 11 4.3.5 LaTex 11 4.3.6 Muscle 11 4.3.7 Pymol 11 4.4 Note about ET Viewer 11 4.5 Citing this work 11 4.6 About report maker 11 4.7 Attachments 11 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1w25): Title: Response regulator pled in complex with c-digmp Compound: Mol id: 1; molecule: stalked-cell differentiation control- ling protein; chain: a, b; synonym: diguanylate cyclase; engineered: yes Organism, scientific name: Caulobacter Vibrioides; 1w25 contains a single unique chain 1w25A (454 residues long) and its homologue 1w25B. CONTENTS 1 Introduction 1 2 CHAIN 1W25A 2.1 Q9A5I5 overview 2 Chain 1w25A 1 2.1 Q9A5I5 overview 1 From SwissProt, id Q9A5I5, 97% identical to 1w25A: 2.2 Multiple sequence alignment for 1w25A 1 Description: Response regulator pleD (Stalked-cell differentiation 2.3 Residue ranking in 1w25A 1 controlling protein) [Includes: Diguanylate cyclase (EC 4.6.1.-) 2.4 Top ranking residues in 1w25A and their position on (DGC)]. the structure 2 Organism, scientific name: Caulobacter crescentus. 2.4.1 Clustering of residues at 25% coverage. 2 Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Caulob- 2.4.2 Overlap with known functional surfaces at acterales; Caulobacteraceae; Caulobacter. 25% coverage. 3 Function: Response regulator that is part of a signal transduction 2.4.3 Possible novel functional surfaces at 25% pathway controlling cell differentiation in the swarmer-to-stalked cell coverage. 8 transition. Function: Catalyzes the condensation of two GTP molecules to the 3 Notes on using trace results 10 cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary 3.1 Coverage 10 messenger. 3.2 Known substitutions 10 Catalytic activity: 2 GTP = 3’,5’-cyclic di-GMP + 2 diphosphate. 3.3 Surface 10 Enzyme regulation: Allosterically inhibited by the product c-di- 3.4 Number of contacts 10 GMP. 3.5 Annotation 10 Subunit: Homodimer. Inactive monomer in solution. 3.6 Mutation suggestions 10 Subcellular location: Cytoplasmic. Phosphorylated pleD localizes to the differentiating pole. 4 Appendix 10 Domain: PleD is activated by phosphorylation at the first response 4.1 File formats 10 regulatory domain, which induces dimerization mediated by the two 4.2 Color schemes used 10 response regulatory domains and allows the two substrate-binding 4.3 Credits 10 sites to approach each other and the condensation reaction to occur 1 Lichtarge lab 2006 (Probable). The diguanylate cyclase activity is harbored by the GGDEF domain. Ptm: Phosphorylated by pleC and divJ. Phosphorylation stimulates cyclase activity. Similarity: Contains 1 GGDEF domain. Similarity: Contains 2 response regulatory domains. 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 1w25A For the chain 1w25A, the alignment 1w25A.msf (attached) with 164 Fig. 1. Residues 2-228 in 1w25A colored by their relative importance. (See sequences was used. The alignment was downloaded from the HSSP Appendix, Fig.14, 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 1w25A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 164 Total number of residues: 68534 Smallest: 342 Largest: 454 Average length: 417.9 Alignment length: 454 Average identity: 30% Most related pair: 99% Most unrelated pair: 6% Fig. 2. Residues 229-455 in 1w25A colored by their relative importance. (See Most distant seq: 30% Appendix, Fig.14, for the coloring scheme.) Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 15% prokaryotic sequences. (Descripti- ons of some sequences were not readily available.) The file contai- ning the sequence descriptions can be found in the attachment, under the name 1w25A.descr. 2.3 Residue ranking in 1w25A The 1w25A sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues in 1w25A can be found in the file called 1w25A.ranks sorted in the attachment. 2.4 Top ranking residues in 1w25A 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 1w25A 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. 4 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.4 are composed of the residues listed in Table 1. 2 Table 1. continued cluster size member color residues red 73 288,289,292,294,295,296,297 299,300,301,302,303,307,323 324,325,327,328,329,330,331 332,334,335,336,338,339,340 343,344,346,347,351,353,354 359,362,365,366,368,369,370 371,372,373,374,375,376,377 384,388,389,390,391,392,395 412,414,415,416,417,430,434 435,437,438,439,441,442,445 446,447,449 blue 23 5,6,7,8,9,10,14,18,22,25,29 32,35,38,39,47,48,50,51,53 78,105,112 yellow 10 91,94,95,98,99,101,250,260 261,264 green 3 278,279,282 purple 2 244,247 azure 2 271,272 Fig. 3. Residues in 1w25A, colored by their relative importance. Clockwise: front, back, top and bottom views. Table 1. Clusters of top ranking residues in 1w25A. 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. 5GP binding site. Table 2 lists the top 25% of residues at the interface with 1w25B5GP501 (5gp). 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 antn (%) bb (A˚ ) 332 K K(96)SH 0.04 5/0 4.62 site QNW Table 2. The top 25% of residues in 1w25A at the interface with 5GP.(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. 4. Residues in 1w25A, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for Table 3. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. res type disruptive mutations 332 K (Y)(T)(FW)(CG) Table 1. cluster size member Table 3. List of disruptive mutations for the top 25% of residues in color residues 1w25A, that are at the interface with 5GP. continued in next column Figure 5 shows residues in 1w25A colored by their importance, at the interface with 1w25B5GP501. 3 Fig. 5. Residues in 1w25A, at the interface with 5GP, colored by their relative Fig. 6. Residues in 1w25A, at the interface with 5GP, colored by their relative importance. The ligand (5GP) is colored green. Atoms further than 30A˚ away importance. The ligand (5GP) 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 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 ligand were removed. (See Appendix for the coloring scheme for the protein chain 1w25A.) chain 1w25A.) 5GP binding site. Table 4 lists the top 25% of residues at the Figure 6 shows residues in 1w25A colored by their importance, at the interface with 1w25A5GP503 (5gp). The following table (Table 5) interface with 1w25A5GP503. suggests possible disruptive replacements for these residues (see Interface with 1w25B.Table 6 lists the top 25% of residues at Section 3.6). the interface with 1w25B. The following table (Table 7) suggests possible disruptive replacements for these residues (see Section 3.6). Table 4. res type subst’s cvg noc/ dist antn Table 6. (%) bb (A˚ ) res type subst’s cvg noc/ dist ˚ 359 R R(84). 0.09 14/0 2.84 site (%) bb (A) H(1) 288 L Q(3) 0.19 35/0 1.82 P(3) L(42) G(2)F M(22) E(1)D E(4) S(1)T A(12) K(1)NQ R(2) G(1) .(3) Table 4. The top 25% of residues in 1w25A at the interface with F(1)VWK 5GP.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each YTH(1)C type in the bracket; noc/bb: number of contacts with the ligand, with the num- 25 E A(18) 0.21 19/5 3.22 ber of contacts realized through backbone atoms given in the bracket; dist: E(45) distance of closest apporach to the ligand.
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