Primary Citation PubMed: 23022727
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Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
(2012) Nat Struct Mol Biol 19
PubMed: 23022727 | PubMedCentral: PMC3492516 | DOI: 10.1038/nsmb.2388
Protein Data Bank: Coordinates and structure factors for the structure have been deposited with accession code 4GFH.
Publication Year: 2012
Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
(2013) Nucleic Acids Res 41
PubMed: 23965305 | PubMedCentral: PMC3834822 | DOI: 10.1093/nar/gkt749
In the yeast topo II structure, the ATPase domains are locked with ADPNP into a dimerized state in the absence of a T-segment, and the DNA gate is trapped in the cleaved state using a suicide DNA subs... rate ( Figure 9 B, PDB entry 4GFH) ( 23 ).
Publication Year: 2013
The structural basis of ATP as an allosteric modulator.
(2014) PLoS Comput Biol 10
PubMed: 25211773 | PubMedCentral: PMC4161293 | DOI: 10.1371/journal.pcbi.1003831
Glycogen phosphorylase Homo sapiens 1FA9 2.40 34 ATP sulfurylase Penicillium chrysogenum 1I2D 2.81 43 Chaperonin GroEL Escherichia coli 1KP8 2.00 17 Phosphofructokinase 1 Escherichia coli 1PFK 2.40 44... MutS Escherichia coli 1W7A 2.27 16 DnaA Aquifex aeolicus 2HCB 3.51 41 Uridine monophosphate kinase Bacillus anthracis 2JJX 2.82 22 Cytosolic 5’-nucleotidase II Homo sapiens 2XCW 1.90 73 ClpX Escherichia coli 3HWS 3.25 45 Ribonucleotide reductase Escherichia coli 3R1R 3.00 74 Aspartate carbamoyltransferase Escherichia coli 4AT1 2.60 75 P2X 4 ion channel Danio rerio 4DW1 2.80 19 DNA Topoisomerase II Saccharomyces cerevisiae 4GFH 4.41 42 Allosteric ATP-binding sites are less conserved than substrate ATP-binding sites To elucidate differences in the evolutionary characteristics of allosteric and substrate ATP-binding sites, we systematically explored the sequence conservation of ATP-binding sites in the ATP allosteric and substrate datasets.
Inspection of these ATP molecules reveals that seven cases adopt compact conformations (PDB: 1FA9, 1I2D, 1PFK, 3HWS, 2XCW, 3R1R, and 4DW1), while the remaining six cases adopt the extended conformations (PDB: 1W7A, 4AT1, 4GFH, 2HCB, 2JJX, and 1KP8).
PDB entry Adenine Ribose Triphosphate H-bonds Hydrophobic H-bonds H-bonds/Electrostatic 1FA9 Y75 / / R193, D227, R242, R309, R310 1I2D K527 F446, F529 / K409, D434, R437, R451, I477 1KP8 N479, A480 P33, I493 G415, D495 G32, D87, G88, T89, T90, T91 1PFK / K214 A ,Y55 B / R154 A , K213 A , R21 B , R25 B , R54 B 1W7A I597 F596, H760 / M617, G619, K620, S621, T622, E694 2HCB F88 I89 H127 G124, K125, T126, H127, D181, R277 2JJX N107 A , A110 A E111 A , I114 B R99 A , R117 A , Y126 A , R117 B , H120 B 2XCW N154, Q453 F354, I152 / R144, D145, R456, Y457 3HWS I79 L127, L317, I325 / G122, S123, G124, K125, T126, R370 3R1R E15, R16, N18 V7, I17, I22 I22 K9, E15, K21, T55, K91 4AT1 I12, K60, Y89 V91 / K94 4DW1 / R143 / N296, R298, K316 4GFH N99 I104, R77 S127, S128 S127, N129, R141, K147, K367, Q365 For example, in the P2X 4 ion channel ( Figure S4A ), residues Asn296, Arg298, and Lys316 from both the unbound (PDB: 4DW0) and ATP-bound (PDB: 4DW1) structures engage in hydrogen bonding/electrostatic interactions with the triphosphate in ATP, revealing marginal conformational changes proximal to the triphosphate in ATP.
Publication Year: 2014
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