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1 Acta Cryst. (2014). D70, doi: /s Supporting information Volume 70 (2014) Supporting information for article: Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N 5 )-carboxyaminoimidazole ribonucleotide synthase (PurK) of Bacillus anthracis Micheal L. Tuntland, Bernard D. Santarsiero, Michael E. Johnson and Leslie W.-M. Fung
2 Table S1: Table of ligand atom contacts and distances for ligands in 3QFF, 3R5H and 3V4S.
3 3QFF (ADP) ChA (Active Site 1) ChB (Active Site 2) 3R5H (ADP) ChA (Active Site 3) ChB (Active Site 4) 3V4S (ADP/ATP) ChA (Active Site 5) ChB (Active Site 6) ADP/ATP N1 V185(N) 2.7 V185(N) 2.8 V185(N) 2.8 V185(N) 2.8 V185(N) 2.7 V185(N) 2.9 N3 H2O H2O H2O N6 E182(OE2) 2.8 E182(OE2) 3.1 E182(OE2) 2.9 E182(OE2) 3.0 K183(O) 2.8 K183(O) 3.0 K183(O) 2.8 K183(O) 3.1 K183(O) 3.0 K183(O) 3.0 N7 N9 O2' E190(OE1) 2.7 E190(OE1) 2.8 E190(OE1) 2.7 H2O E190(OE1) 2.6 O3' E190(OE1) 3.1 E190(OE2) 2.8 E190(OE2) 3.0 E190(OE2) 2.7 E190(OE2) 2.8 E190(OE2) 2.6 H2O H2O O4' N216(ND2) 3.3 N216(ND2) 3.1 O5' Q158(OE1) 3.2 H2O O1A H2O Mg Mg Mg Mg K183(O) 3.0 H2O H2O H2O H2O N267(ND2) 2.9 N267(ND2) 3.0 N267(ND2) 3.2 N267(ND2) 3.1 N267(ND2) 3.2 N267(ND2) 3.2 H2O O2A R107(NH2) 3.0 R107(NH2) 3.1 K147(NZ) 2.8 K147(NZ) 2.8 K147(NZ) 2.7 K147(NZ) 2.6 K147(NZ) 2.8 K147(NZ) 2.8 Q158(NE2) 3.0 E268(OE2) 2.9 O3A R107(NH2) 2.7 R107(NH1) 3.0 H2O O1B H2O H2O Y153(N) 3.3 E255(OE1) 2.7 G155(N) 2.8 G155(N) 2.8 E268(OE1) 2.9 E268(OE1) 2.9 N216(ND2) 3.1 E268(OE2) 2.9 O2B R107(NH1) 2.7 E255(OE2) 3.0 H2O R107(NH1) 2.5 R107(NH2) 2.7 E268(OE1) 3.0 E268(OE2) 3.1 E268(OE1) 2.9 E268(OE2) 3.0 E268(OE1) 3.0 H2O H2O O3B H2O Mg Mg Mg H2O H2O H213(NE2) 2.8 N216(OD1) 3.0 R107(NH2) 3.0 E268(OE1) 3.3 H2O H2O O1G E255(OE2) 3.2 Mg H2O O2G D154(N) 2.8 H2O H2O O3G H2O H2O QFF (ADP) 3R5H (ADP) 3V4S (ADP/ATP) ChA (Active Site 1) ChB (Active Site 2) ChA (Active Site 3) ChB (Active Site 4) ChA (Active Site 5) ChB (Active Site 6) Mg 2+ H2O H2O H2O H2O H2O H2O H2O H2O H2O H2O E255(OE1) 2.6 E255(OE1) 2.3 E268(OE1) 2.2 E268(OE1) 2.2 E268(OE1) 2.0 E268(OE1) 2.2 ADP (O1A) 2.1 ADP (O1A) 2.4 ADP (O1A) 2.1 ATP (O1A) 2.1 ADP (O3B) 2.7 ADP (O3B) 3.2 ADP (O3B) 2.1 ATP (O1G) 2.2 Mg 2+ at L269 H2O 183 3QFF (ADP) 3R5H (ADP) ChA (Active Site 1) ChB (Active Site 2) ChA (Active Site 3) ChB (Active Site 4) AIR N3 Y153(OH) 3.0 H2O N6 H2O H2O H2O H2O O2' E76(OE1) 2.5 E76(OE1) 2.5 L19(N) 3.1 O3' E76(OE2) 2.5 E76(OE2) 2.6 H2O H2O H2O O4' Q18(OE1) 3.4 H2O O5' K340(NZ) 3.3 H2O H2O O6 H2O R347(NH2) 3.0 H2O H2O O7 R347(NH2) 3.1 K340(NZ) 2.9 R347(NE) 2.7 H2O H2O O8 R347(NE) 2.5 H2O V4S (ADP/ATP) ChA (Active Site 5) ChB (Active Site 6) 3QFF (ADP) 3R5H (ADP) 3V4S (ADP/ATP) ChA (Active Site 1) ChB (Active Site 2) ChA (Active Site 3) ChB (Active Site 4) ChA (Active Site 5) ChB (Active Site 6) HCO 3 O1 (NH2) 2.8 (NH2) 2.8 H274(NE2) 3.3 H274(NE2) 3.4 H2O O2 (NH1) 2.8 (NH1) 2.7 H2O H2O O3 K348(NZ) 3.4 K348(NZ) 3.4 H274(NE2) 3.4 H274(NE2) 3.4 *Distances in Angstroms (Å) *H2O in RED believed to be involved in transfer in our proposed mechanism
4 Figure S1: Alignment of bapurk amino acid sequence to that of 11 other PurKs for differing organisms; including from Archaea (Sulfolobus solfataricus), Bacteria (Gram-negative; Escherichia coli, Vibrio cholerae, Aquifex aeolicus; Gram-positive; Bacillus subtilis, Staphylococcus aureus; No Gram-stain; Mycobacterium leprae, Mycobacterium tuberculosis), Fungi (Aspergillus clavatus, Saccharomyces cerevisiae) and Plantae (Vigna aconitifolia). White letters in black boxes are strictly conserved residues throughout the 12 organisms. Loops are boxed and color-coded as in Fig 1A of text. A-Loop (green), B-Loop (blue), ABC-Loop (orange), DT-Loop (purple), J-Loop (cyan), P-Loop (red) and Ω-Loop (yellow).
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7 Figure S2: Shown is a series of omit maps that were generated by setting the occupancy of the bicarbonate atoms to zero and re-refining the structure 3V4S-B. The top panel shows all three maps; mf o -DF c (dark blue), 2mF o -DF c (orange) and 3mF o -2DF c (teal) at 3.5, 1.5 and 2.5 σ, (0.28, 0.43, and 0.78 e - /Å 3 ) respectively, from a top-down view. The enzyme (green) is depicted as a cartoon representation, with the side chain of shown in a stick representation as an anchor for orientation. The bottom three panels show the individual maps; mf o -DF c, 2mF o -DF c and 3mF o -2DF c (left to right) rotated 90 to give the side view, confirming the correct trigonal planar density. mf o -DF c at 3.5 σ 2mF o -DF c at 1.5 σ 3mF o -2DF c at 2.5 σ
8 Figure S3: Shown is a mf o -DF c omit map (dark blue mesh) focused on HCO 3 - (red and yellow) and its proximity to (cyan) and K348 (orange) from 3V4S-B. The map was generated by setting the occupancy of all the atoms from HCO 3 -, and K348 to zero and re-refining the structure. The mf o -DF c map is contoured to 3.0 σ (0.24 e - /Å 3 ). K348 HCO 3 - mf o -DF c at 3.0 σ
9 Figure S4: Shown is the environment of water 479 from 3R5H-B (same position as water 41 in 3V4S-B) that acts as a base in our mechanism, we propose that a hydrogen is removed by K348 (orange) to allow water 479 to deprotonate the exocylic amine of AIR. The water displays typical tetrahedral geometry, interacting with the O2 atom of bicarbonate and both of the amine groups from AIR and K348 of the modeled active site. It also hydrogen bonds with water 385 of 3R5H-B. Dashed lines are possible hydrogen bonds available within 3.4 Å.
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