Pages 1–14 1go4 Evolutionary trace report by report maker May 8, 2010 4 Notes on using trace results 12 4.1 Coverage 12 4.2 Known substitutions 12 4.3 Surface 12 4.4 Number of contacts 12 4.5 Annotation 12 4.6 Mutation suggestions 12 5 Appendix 12 5.1 File formats 12 5.2 Color schemes used 12 5.3 Credits 13 5.3.1 Alistat 13 5.3.2 CE 13 5.3.3 DSSP 13 5.3.4 HSSP 13 5.3.5 LaTex 13 5.3.6 Muscle 13 5.3.7 Pymol 13 5.4 Note about ET Viewer 13 5.5 Citing this work 13 CONTENTS 5.6 About report maker 13 5.7 Attachments 13 1 Introduction 1 2 Chain 1go4G 1 1 INTRODUCTION 2.1 Q9Y6D9 overview 1 From the original Protein Data Bank entry (PDB id 1go4): 2.2 Multiple sequence alignment for 1go4G 1 Title: Crystal structure of mad1-mad2 reveals a conserved mad2 2.3 Residue ranking in 1go4G 2 binding motif in mad1 and cdc20. 2.4 Top ranking residues in 1go4G and their position on Compound: Mol id: 1; molecule: mitotic spindle assembly check- the structure 2 point protein mad2a; chain: a, b, c, d; synonym: mad2, mad2-like 1, 2.4.1 Clustering of residues at 25% coverage. 2 hsmad2; engineered: yes; mutation: yes; mol id: 2; molecule: mad1 2.4.2 Overlap with known functional surfaces at (mitotic arrest deficient)-like 1; chain: e, f, g, h; fragment: residues 25% coverage. 3 485-584; engineered: yes 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Homo Sapiens; coverage. 6 1go4 contains unique chains 1go4G (100 residues) and 1go4A (196 residues) 1go4H, 1go4F, and 1go4E are homologues of chain 1go4G. 3 Chain 1go4A 8 1go4B, 1go4C, and 1go4D are homologues of chain 1go4A. 3.1 Q4R7B3 overview 8 3.2 Multiple sequence alignment for 1go4A 8 2 CHAIN 1GO4G 3.3 Residue ranking in 1go4A 8 3.4 Top ranking residues in 1go4A and their position on 2.1 Q9Y6D9 overview the structure 8 From SwissProt, id Q9Y6D9, 87% identical to 1go4G: 3.4.1 Clustering of residues at 25% coverage. 8 Description: Mitotic spindle assembly checkpoint protein MAD1 3.4.2 Overlap with known functional surfaces at (Mitotic arrest deficient-like protein 1) (MAD1-like 1) (Mitotic 25% coverage. 9 checkpoint MAD1 protein-homolog) (HsMAD1) (hMAD1) (Tax 3.4.3 Possible novel functional surfaces at 25% binding protein-181). coverage. 9 Organism, scientific name: Homo sapiens (Human). 1 Lichtarge lab 2006 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. Function: Component of the spindle-assembly checkpoint that pre- vents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. Has a role in the correct positio- ning of the septum. Required for anchoring MAD2L1 to the nuclear Fig. 1. Residues 485-584 in 1go4G colored by their relative importance. (See periphery. Appendix, Fig.20, for the coloring scheme.) Subunit: Homodimer. Heterodimerizes with MAD2L1 in order to form a tetrameric MAD1L1-MAD2L1 core complex. Perturbation of Furthermore, 4% of residues show as conserved in this alignment. the original MAD1L1-MAD2L1 structure by the spindle checkpoint The alignment consists of 63% eukaryotic ( 63% vertebrata) may decrease MAD2L1 affinity for MAD1L1. CDC20 can compete sequences. (Descriptions of some sequences were not readily availa- with MAD1L1 for MAD2L1 binding, until the attachment and/or ble.) The file containing the sequence descriptions can be found in tension dampen the checkpoint signal, preventing further release of the attachment, under the name 1go4G.descr. MAD2L1 on to CDC20. Also able to interact with the BUB1/BUB3 complex and the viral Tax protein. 2.3 Residue ranking in 1go4G Subcellular location: Nuclear. From the beginning to the end of mit- The 1go4G sequence is shown in Fig. 1, with each residue colored osis, it is seen to move from a diffusely nuclear distribution to the according to its estimated importance. The full listing of residues centrosome, to the spindle midzone and finally to the midbody. in 1go4G can be found in the file called 1go4G.ranks sorted in the Alternative products: attachment. Event=Alternative splicing; Named isoforms=2; Name=1; Syn- onyms=MAD1a; IsoId=Q9Y6D9-1; Sequence=Displayed; Name=2; 2.4 Top ranking residues in 1go4G and their position on IsoId=Q9Y6D9-2; Sequence=VSP 011637; Note=No experimental the structure confirmation available; In the following we consider residues ranking among top 25% of Tissue specificity: Expressed weakly at G0/G1 and highly at late S residues in the protein . Figure 2 shows residues in 1go4G colored and G2/M phase. by their importance: bright red and yellow indicate more conser- Induction: Increased by TP53. ved/important residues (see Appendix for the coloring scheme). A Ptm: Phosphorylated; by BUB1. Become hyperphosphorylated in Pymol script for producing this figure can be found in the attachment. late S through M phases or after mitotic spindle damage. Disease: Defects in MAD1L1 are involved in the development and/or progression of various types of cancer. Similarity: Belongs to the MAD1 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 1go4G For the chain 1go4G, the alignment 1go4G.msf (attached) with 11 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 1go4G.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 11 Total number of residues: 1074 Smallest: 91 Largest: 100 Average length: 97.6 Alignment length: 100 Fig. 2. Residues in 1go4G, colored by their relative importance. Clockwise: Average identity: 43% front, back, top and bottom views. Most related pair: 98% Most unrelated pair: 19% Most distant seq: 35% 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they 2 belong to. The clusters in Fig.3 are composed of the residues listed Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) 532 Q Q(81) 0.06 17/0 1.69 R(18) 522 L L(90) 0.13 34/32 1.35 A(9) 531 L L(90) 0.13 2/2 3.85 I(9) 527 E E(90) 0.24 125/72 0.41 M(9) Table 2. The top 25% of residues in 1go4G at the interface with 1go4E. (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 523 E (FWH)(YVCARG)(T)(SNKLPI) 532 Q (Y)(T)(FW)(SVCAHG) Fig. 3. Residues in 1go4G, colored according to the cluster they belong to: 522 L (YR)(H)(TKE)(SQCDG) red, followed by blue and yellow are the largest clusters (see Appendix for 531 L (YR)(TH)(SKECG)(FQWD) the coloring scheme). Clockwise: front, back, top and bottom views. The 527 E (H)(FYW)(CRG)(TVA) corresponding Pymol script is attached. Table 3. List of disruptive mutations for the top 25% of residues in in Table 1. 1go4G, that are at the interface with 1go4E. Table 1. cluster size member color residues red 6 564,567,568,570,571,572 blue 5 501,504,506,508,509 yellow 5 522,523,527,531,532 green 3 540,541,542 purple 2 549,553 azure 2 514,515 Table 1. Clusters of top ranking residues in 1go4G. 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 1go4E.By analogy with 1go4H – 1go4E interface. Table 2 lists the top 25% of residues at the interface with 1go4E. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 4.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 523 E E(100) 0.04 69/46 1.86 continued in next column Fig. 4. Residues in 1go4G, at the interface with 1go4E, colored by their rela- tive importance. 1go4E is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 1go4G.) 3 Figure 4 shows residues in 1go4G colored by their importance, at the Interface with 1go4B.Table 6 lists the top 25% of residues at the interface with 1go4E. interface with 1go4B. The following table (Table 7) suggests possible Interface with 1go4C.By analogy with 1go4F – 1go4C interface. disruptive replacements for these residues (see Section 4.6). Table 4 lists the top 25% of residues at the interface with 1go4C. The following table (Table 5) suggests possible disruptive replacements Table 6. for these residues (see Section 4.6). res type subst’s cvg noc/ dist (%) bb (A˚ ) Table 4. 496 E D(9) 0.19 39/1 2.97 res type subst’s cvg noc/ dist E(81) ˚ (%) bb (A) A(9) 531 L L(90) 0.13 5/0 3.47 I(9) Table 6.