Pages 1–5 2qnk Evolutionary trace report by report maker September 16, 2008

4.3.3 DSSP 4 4.3.4 HSSP 4 4.3.5 LaTex 4 4.3.6 Muscle 4 4.3.7 Pymol 4 4.4 Note about ET Viewer 4 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 5

1 INTRODUCTION From the original entry (PDB id 2qnk): Title: Crystal structure of human 3-hydroxyanthranilate 3,4- dioxy- genase Compound: Mol id: 1; molecule: 3-hydroxyanthranilate 3,4- dioxygenase; chain: a; synonym: 3-hao, 3-hydroxyanthranilic acid CONTENTS dioxygenase, 3- hydroxyanthranilate ; ec: 1.13.11.6; engi- neered: yes 1 Introduction 1 Organism, scientific name: Homo Sapiens; 2qnk contains a single unique chain 2qnkA (286 residues long). 2 Chain 2qnkA 1 2.1 Q53QZ7 overview 1 2.2 Multiple sequence alignment for 2qnkA 1 2.3 Residue ranking in 2qnkA 1 2.4 Top ranking residues in 2qnkA and their position on the structure 2 2 CHAIN 2QNKA 2.4.1 Clustering of residues at 23% coverage. 2 2.1 Q53QZ7 overview 2.4.2 Overlap with known functional surfaces at From SwissProt, id Q53QZ7, 97% identical to 2qnkA: 23% coverage. 2 Description: Hypothetical protein HAAO. 3 Notes on using trace results 3 Organism, scientific name: Homo sapiens (Human). 3.1 Coverage 3 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 3.2 Known substitutions 3 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; 3.3 Surface 3 Catarrhini; Hominidae; Homo. 3.4 Number of contacts 3 3.5 Annotation 3 3.6 Mutation suggestions 3 2.2 Multiple sequence alignment for 2qnkA 4 Appendix 4 For the chain 2qnkA, the alignment 2qnkA.msf (attached) with 11 4.1 File formats 4 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 4 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 4 using Muscle program. It can be found in the attachment to this 4.3.1 Alistat 4 report, under the name of 2qnkA.msf. Its statistics, from the alistat 4.3.2 CE 4 program are the following:

1 Lichtarge lab 2006 Fig. 1. Residues 1-143 in 2qnkA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.)

Fig. 2. Residues 144-286 in 2qnkA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.)

Fig. 3. Residues in 2qnkA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 11 Total number of residues: 3110 Smallest: 276 Largest: 286 Average length: 282.7 Alignment length: 286 Average identity: 54% Most related pair: 97% Most unrelated pair: 36% Most distant seq: 49%

Furthermore, 22% of residues show as conserved in this alignment. The alignment consists of 90% eukaryotic ( 63% vertebrata) 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 2qnkA.descr. 2.3 Residue ranking in 2qnkA The 2qnkA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 2qnkA can be found in the file called 2qnkA.ranks sorted in the attachment. 2.4 Top ranking residues in 2qnkA and their position on Fig. 4. Residues in 2qnkA, colored according to the cluster they belong to: the structure red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The In the following we consider residues ranking among top 23% of resi- corresponding Pymol script is attached. dues in the protein (the closest this analysis allows us to get to 25%). Figure 3 shows residues in 2qnkA colored by their importance: bright red and yellow indicate more conserved/important residues (see in Table 1. 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 23% coverage. Fig. 4 shows the top 23% of all residues, this time colored according to clusters they belong to. The clusters in Fig.4 are composed of the residues listed

2 Table 1. cluster size member color residues red 56 14,18,20,21,22,23,24,25,31 32,38,39,40,41,43,44,45,47 49,50,51,52,53,55,57,60,61 64,74,77,80,81,86,88,91,92 93,94,95,101,102,103,105,106 108,112,114,117,129,131,132 141,143,169,180,279 blue 4 120,127,157,159

Table 1. Clusters of top ranking residues in 2qnkA.

2.4.2 Overlap with known functional surfaces at 23% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Nickel (ii) ion . Table 2 lists the top 23% of residues at the interface with 2qnkANI287 (nickel (ii) ion). The following table (Table 3) suggests possible disruptive replacements for these residues Fig. 5. Residues in 2qnkA, at the interface with nickel (ii) ion, colored by (see Section 3.6). their relative importance. The ligand (nickel (ii) ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on Table 2. the line of sight to the ligand were removed. (See Appendix for the coloring res type subst’s cvg noc/ dist scheme for the protein chain 2qnkA.) (%) bb (A˚ ) 47 H H(100) 0.23 6/0 2.13 49 E E(100) 0.23 2/0 4.51 53 E E(100) 0.23 4/0 2.18 3 NOTES ON USING TRACE RESULTS 91 H H(100) 0.23 5/0 2.06 3.1 Coverage 105 E E(100) 0.23 1/0 4.21 Trace results are commonly expressed in terms of coverage: the resi- due is important if its “coverage” is small - that is if it belongs to Table 2. The top 23% of residues in 2qnkA at the interface with nickel some small top percentage of residues [100% is all of the residues (ii) ion.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each in a chain], according to trace. The ET results are presented in the type in the bracket; noc/bb: number of contacts with the ligand, with the num- form of a table, usually limited to top 25% percent of residues (or ber of contacts realized through backbone atoms given in the bracket; dist: to some nearby percentage), sorted by the strength of the presumed distance of closest apporach to the ligand. ) evolutionary pressure. (I.e., the smaller the coverage, the stronger the pressure on the residue.) Starting from the top of that list, mutating a couple of residues should affect the protein somehow, with the exact effects to be determined experimentally.

Table 3. res type disruptive 3.2 Known substitutions mutations One of the table columns is “substitutions” - other amino acid types 47 H (E)(TQMD)(SNKVCLAPIG)(YR) seen at the same position in the alignment. These amino acid types 49 E (FWH)(YVCARG)(T)(SNKLPI) may be interchangeable at that position in the protein, so if one wants 53 E (FWH)(YVCARG)(T)(SNKLPI) to affect the protein by a point mutation, they should be avoided. For 91 H (E)(TQMD)(SNKVCLAPIG)(YR) example if the substitutions are “RVK” and the original protein has 105 E (FWH)(YVCARG)(T)(SNKLPI) an R at that position, it is advisable to try anything, but RVK. Conver- sely, when looking for substitutions which will not affect the protein, Table 3. List of disruptive mutations for the top 23% of residues in one may try replacing, R with K, or (perhaps more surprisingly), with 2qnkA, that are at the interface with nickel (ii) ion. V. The percentage of times the substitution appears in the alignment is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough Figure 5 shows residues in 2qnkA colored by their importance, at the guide - due to rounding errors these percentages often do not add up interface with 2qnkANI287. to 100%.

3 3.3 Surface To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by 2 at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require COVERAGE that these residues form a “cluster” of residues which have neighbor within 5A˚ from any of their heavy atoms. V Note, however, that, if our picture of protein evolution is correct, 100% 50% 30% 5% the neighboring residues which are not surface accessible might be equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choo- sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) V 3.4 Number of contacts RELATIVE IMPORTANCE Another column worth noting is denoted “noc/bb”; it tells the num- ber of contacts heavy atoms of the residue in question make across the interface, as well as how many of them are realized through the Fig. 6. Coloring scheme used to color residues by their relative importance. backbone atoms (if all or most contacts are through the backbone, mutation presumably won’t have strong impact). Two heavy atoms • are considered to be “in contact” if their centers are closer than 5A˚ . variability has two subfields: 1. number of different amino acids appearing in in this column 3.5 Annotation of the alignment If the residue annotation is available (either from the pdb file or 2. their type from other sources), another column, with the header “annotation” • rho ET score - the smaller this value, the lesser variability of appears. Annotations carried over from PDB are the following: site this position across the branches of the tree (and, presumably, (indicating existence of related site record in PDB ), S-S (disulfide the greater the importance for the protein) bond forming residue), hb (hydrogen bond forming residue, jb (james • bond forming residue), and sb (for salt bridge forming residue). cvg coverage - percentage of the residues on the structure which have this rho or smaller 3.6 Mutation suggestions • gaps percentage of gaps in this column Mutation suggestions are completely heuristic and based on comple- mentarity with the substitutions found in the alignment. Note that 4.2 Color schemes used they are meant to be disruptive to the interaction of the protein The following color scheme is used in figures with residues colored with its ligand. The attempt is made to complement the following by cluster size: black is a single-residue cluster; clusters composed of properties: small [AV GST C], medium [LP NQDEMIK], large more than one residue colored according to this hierarchy (ordered [W F Y HR], hydrophobic [LP V AMW F I], polar [GT CY ]; posi- by descending size): red, blue, yellow, green, purple, azure, tur- tively [KHR], or negatively [DE] charged, aromatic [W F Y H], quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, long aliphatic chain [EKRQM], OH-group possession [SDET Y ], bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, and NH2 group possession [NQRK]. The suggestions are listed DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, according to how different they appear to be from the original amino tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. acid, and they are grouped in round brackets if they appear equally The colors used to distinguish the residues by the estimated disruptive. From left to right, each bracketed group of amino acid evolutionary pressure they experience can be seen in Fig. 6. types resembles more strongly the original (i.e. is, presumably, less disruptive) These suggestions are tentative - they might prove disrup- 4.3 Credits tive to the fold rather than to the interaction. Many researcher will 4.3.1 Alistat alistat reads a multiple sequence alignment from the choose, however, the straightforward alanine mutations, especially in file and shows a number of simple statistics about it. These stati- the beginning stages of their investigation. stics include the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, and the 4 APPENDIX alignment length (e.g. including gap characters). Also shown are 4.1 File formats some percent identities. A percent pairwise alignment identity is defi- ned as (idents / MIN(len1, len2)) where idents is the number of Files with extension “ranks sorted” are the actual trace results. The exact identities and len1, len2 are the unaligned lengths of the two fields in the table in this file: sequences. The ”average percent identity”, ”most related pair”, and • alignment# number of the position in the alignment ”most unrelated pair” of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant • residue# residue number in the PDB file seq” is calculated by finding the maximum pairwise identity (best • type amino acid type relative) for all N sequences, then finding the minimum of these N • rank rank of the position according to older version of ET numbers (hence, the most outlying sequence). alistat is copyrighted

4 by HHMI/Washington University School of Medicine, 1992-2001, http://mammoth.bcm.tmc.edu/traceview/ and freely distributed under the GNU General Public License. The viewer is self-unpacking and self-installing. Input files to be used 4.3.2 CE To map ligand binding sites from different with ETV (extension .etvx) can be found in the attachment to the source structures, report maker uses the CE program: main report. http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) ”Protein structure alignment by incremental combinatorial extension 4.5 Citing this work (CE) of the optimal path . Protein Engineering 11(9) 739-747. The method used to rank residues and make predictions in this report 4.3.3 DSSP In this work a residue is considered solvent accessi- can be found in Mihalek, I., I. Res,ˇ O. Lichtarge. (2004). ”A Family of 2 ble if the DSSP program finds it exposed to water by at least 10A˚ , Evolution-Entropy Hybrid Methods for Ranking of Protein Residues which is roughly the area needed for one water molecule to come in by Importance” J. Mol. Bio. 336: 1265-82. For the original version the contact with the residue. DSSP is copyrighted by W. Kabsch, C. of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolu- Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version tionary Trace Method Defines Binding Surfaces Common to Protein by [email protected] November 18,2002, Families” J. Mol. Bio. 257: 342-358. report maker itself is described in Mihalek I., I. Res and O. http://www.cmbi.kun.nl/gv/dssp/descrip.html. Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type of service for comparative analysis of proteins.” Bioinformatics 4.3.4 HSSP Whenever available, report maker uses HSSP ali- 22:1656-7. gnment as a starting point for the analysis (sequences shorter than 75% of the query are taken out, however); R. Schneider, A. de 4.6 About report maker Daruvar, and C. Sander. ”The HSSP database of protein structure- report maker was written in 2006 by Ivana Mihalek. The 1D ran- sequence alignments.” Nucleic Acids Res., 25:226–230, 1997. king visualization program was written by Ivica Res.ˇ report maker http://swift.cmbi.kun.nl/swift/hssp/ is copyrighted by Lichtarge Lab, Baylor College of Medicine, Houston. 4.3.5 LaTex The text for this report was processed using LATEX; Leslie Lamport, “LaTeX: A Document Preparation System Addison- 4.7 Attachments Wesley,” Reading, Mass. (1986). The following files should accompany this report: 4.3.6 Muscle When making alignments “from scratch”, report • 2qnkA.complex.pdb - coordinates of 2qnkA with all of its maker uses Muscle alignment program: Edgar, Robert C. (2004), ”MUSCLE: multiple sequence alignment with high accuracy and interacting partners high throughput.” Nucleic Acids Research 32(5), 1792-97. • 2qnkA.etvx - ET viewer input file for 2qnkA • http://www.drive5.com/muscle/ 2qnkA.cluster report.summary - Cluster report summary for 2qnkA 4.3.7 Pymol The figures in this report were produced using • 2qnkA.ranks - Ranks file in sequence order for 2qnkA Pymol. The scripts can be found in the attachment. Pymol • 2qnkA.clusters - Cluster descriptions for 2qnkA is an open-source application copyrighted by DeLano Scien- tific LLC (2005). For more information about Pymol see • 2qnkA.msf - the multiple sequence alignment used for the chain http://pymol.sourceforge.net/. (Note for Windows 2qnkA users: the attached package needs to be unzipped for Pymol to read • 2qnkA.descr - description of sequences used in 2qnkA msf the scripts and launch the viewer.) • 2qnkA.ranks sorted - full listing of residues and their ranking 4.4 Note about ET Viewer for 2qnkA • Dan Morgan from the Lichtarge lab has developed a visualization 2qnkA.2qnkANI287.if.pml - Pymol script for Figure 5 tool specifically for viewing trace results. If you are interested, please • 2qnkA.cbcvg - used by other 2qnkA – related pymol scripts visit:

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