2Dre Lichtarge Lab 2006

Pages 1–8 2dre Evolutionary trace report by report maker September 18, 2010 4.3.1 Alistat 7 4.3.2 CE 7 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 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2dre): Title: Crystal structure of water-soluble chlorophyll protein from lepidium virginicum at 2.00 angstrom resolution Compound: Mol id: 1; molecule: water-soluble chlorophyll protein; CONTENTS chain: a, b, c, d; fragment: residues 1-180 Organism, scientific name: Lepidium Virginicum; 1 Introduction 1 2dre contains a single unique chain 2dreD (177 residues long) and its homologues 2dreA, 2dreC, and 2dreB. 2 Chain 2dreD 1 2.1 O04797 overview 1 2.2 Multiple sequence alignment for 2dreD 1 2.3 Residue ranking in 2dreD 1 2.4 Top ranking residues in 2dreD and their position on 2 CHAIN 2DRED the structure 1 2.4.1 Clustering of residues at 25% coverage. 2 2.1 O04797 overview 2.4.2 Overlap with known functional surfaces at From SwissProt, id O04797, 100% identical to 2dreD: 25% coverage. 3 Description: Water-soluble chlorophyll protein. 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Lepidium virginicum. coverage. 5 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3 Notes on using trace results 6 eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Lepi- 3.1 Coverage 6 dium. 3.2 Known substitutions 6 3.3 Surface 6 3.4 Number of contacts 6 3.5 Annotation 6 2.2 Multiple sequence alignment for 2dreD 3.6 Mutation suggestions 6 For the chain 2dreD, the alignment 2dreD.msf (attached) with 56 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 6 database, and fragments shorter than 75% of the query as well as 4.1 File formats 6 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 6 to this report, under the name of 2dreD.msf. Its statistics, from the 4.3 Credits 7 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 3-179 in 2dreD colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Format: MSF Number of sequences: 56 Total number of residues: 8916 Smallest: 77 Largest: 177 Average length: 159.2 Alignment length: 177 Average identity: 36% Most related pair: 99% Fig. 2. Residues in 2dreD, colored by their relative importance. Clockwise: Most unrelated pair: 13% front, back, top and bottom views. Most distant seq: 35% Furthermore, <1% of residues show as conserved in this alignment. The alignment consists of 76% eukaryotic ( 76% plantae) 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 2dreD.descr. 2.3 Residue ranking in 2dreD The 2dreD sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2dreD can be found in the file called 2dreD.ranks sorted in the attachment. 2.4 Top ranking residues in 2dreD and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 2dreD colored by their importance: bright red and yellow indicate more conserved/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. 3 shows the Fig. 3. Residues in 2dreD, colored according to the cluster they belong to: top 25% of all residues, this time colored according to clusters they red, followed by blue and yellow are the largest clusters (see Appendix for belong to. The clusters in Fig.3 are composed of the residues listed the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. in Table 1. Table 1. Table 1. continued cluster size member cluster size member color residues color residues red 42 7,9,12,15,18,21,22,23,25,31 60,61,62,64,82,83,85,95,96 32,33,34,45,46,48,49,51,59 98,99,109,111,112,113,120 continued in next column 122,124,126,134,135,136,173 continued in next column 2 Table 1. continued cluster size member color residues Table 1. Clusters of top ranking residues in 2dreD. 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 2dreA.Table 2 lists the top 25% of residues at the interface with 2dreA. 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˚ ) 45 C C(96) 0.05 27/17 3.59 S-S L(1) .(1) 46 P P(96) 0.05 4/2 4.74 N(1) .(1) Fig. 4. Residues in 2dreD, at the interface with 2dreA, colored by their relative importance. 2dreA is shown in backbone representation (See Appendix Table 2. The top 25% of residues in 2dreD at the interface with 2dreA. for the coloring scheme for the protein chain 2dreD.) (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 Table 4. continued contacts realized through backbone atoms given in the bracket; dist: distance res type subst’s cvg noc/ dist of closest apporach to the ligand. ) (%) bb (A˚ ) T(21) M(3) Table 3. F(3) res type disruptive I(1) mutations .(1) 45 C (R)(KE)(H)(FWD) 22 F Y(37) 0.21 9/0 3.79 46 P (Y)(R)(TH)(CG) I(33) F(14) Table 3. List of disruptive mutations for the top 25% of residues in 2dreD, H(7) that are at the interface with 2dreA. L(5) .(1) Figure 4 shows residues in 2dreD colored by their importance, at the interface with 2dreA. Table 4. The top 25% of residues in 2dreD at the interface with 2dreC. Interface with 2dreC.Table 4 lists the top 25% of residues at the (Field names: res: residue number in the PDB entry; type: amino acid type; interface with 2dreC. The following table (Table 5) suggests possible substs: substitutions seen in the alignment; with the percentage of each type disruptive replacements for these residues (see Section 3.6). 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 Table 4. of closest apporach to the ligand. ) res type subst’s cvg noc/ dist (%) bb (A˚ ) 61 P P(96) 0.02 7/0 3.91 Table 5. K(1) res type disruptive .(1) mutations 59 G G(96) 0.07 3/3 3.86 61 P (Y)(T)(R)(H) V(1) 59 G (KER)(HD)(Q)(FMW) .(1) 60 L (R)(Y)(H)(T) 60 L L(67) 0.16 1/0 4.81 22 F (K)(E)(Q)(T) continued in next column continued in next column 3 Table 5. continued Table 6. continued res type disruptive res type subst’s cvg noc/ dist mutations (%) bb (A˚ ) .(1) Table 5. List of disruptive mutations for the top 25% of residues in 2dreD, that are at the interface with 2dreC. Table 6. The top 25% of residues in 2dreD at the interface with chlorophyll a.(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 7. res type disruptive mutations 51 R (T)(D)(YVCAG)(S) 59 G (KER)(HD)(Q)(FMW) 60 L (R)(Y)(H)(T) Table 7. List of disruptive mutations for the top 25% of residues in 2dreD, that are at the interface with chlorophyll a. Fig. 5. Residues in 2dreD, at the interface with 2dreC, colored by their relative importance. 2dreC is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 2dreD.) Figure 5 shows residues in 2dreD colored by their importance, at the interface with 2dreC. Chlorophyll a binding site. Table 6 lists the top 25% of residues at the interface with 2dreDCLA1001 (chlorophyll a). The following table (Table 7) suggests possible disruptive replacements for these residues (see Section 3.6). Table 6. res type subst’s cvg noc/ dist (%) bb (A˚ ) 51 R Q(96) 0.06 1/1 4.89 R(1) Fig. 6. Residues in 2dreD, at the interface with chlorophyll a, colored by .(1) their relative importance. The ligand (chlorophyll a) is colored green. Atoms 59 G G(96) 0.07 2/2 4.55 further than 30A˚ away from the geometric center of the ligand, as well as on V(1) the line of sight to the ligand were removed. (See Appendix for the coloring .(1) scheme for the protein chain 2dreD.) 60 L L(67) 0.16 17/2 3.82 T(21) Figure 6 shows residues in 2dreD colored by their importance, at the M(3) interface with 2dreDCLA1001.

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