Citations in PubMed

Primary Citation PubMed: 23022727 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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