2022
DOI: 10.3390/biom12101345
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Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases

Abstract: The P-loop fold nucleoside triphosphate (NTP) hydrolases (also known as Walker NTPases) function as ATPases, GTPases, and ATP synthases, are often of medical importance, and represent one of the largest and evolutionarily oldest families of enzymes. There is still no consensus on their catalytic mechanism. To clarify this, we performed the first comparative structural analysis of more than 3,100 structures of P-loop NTPases that contain bound substrate Mg-NTPs or their analogues. We proceeded on the assumption… Show more

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Cited by 5 publications
(37 citation statements)
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“…As for the analysis presented in in the companion paper [ 30 ], the structures were selected among those PDB entries that matched the following criteria: (1) assigned to InterPro record IPR027417; (2) contained an ATP/GTP molecule, non-hydrolyzable analogue of NTP, or a transition-state analogue; (3) contained at least one Mg 2+ , Mn 2+ , or Ca 2+ ion; and (4) resolution of 5 Å or higher, if applicable. Proteins were assigned to major classes of P-loop NTPases according to their membership in Pfam families [ 9 , 10 ]; see the details in the companion paper [ 30 ]. This search yielded 1474 PDB structures with 3666 catalytic sites in them.…”
Section: Methodsmentioning
confidence: 99%
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“…As for the analysis presented in in the companion paper [ 30 ], the structures were selected among those PDB entries that matched the following criteria: (1) assigned to InterPro record IPR027417; (2) contained an ATP/GTP molecule, non-hydrolyzable analogue of NTP, or a transition-state analogue; (3) contained at least one Mg 2+ , Mn 2+ , or Ca 2+ ion; and (4) resolution of 5 Å or higher, if applicable. Proteins were assigned to major classes of P-loop NTPases according to their membership in Pfam families [ 9 , 10 ]; see the details in the companion paper [ 30 ]. This search yielded 1474 PDB structures with 3666 catalytic sites in them.…”
Section: Methodsmentioning
confidence: 99%
“…We investigated the reliability of each catalytic site by assessing the integrity of the NTP analogue/presence of γ-phosphate mimic, presence of a P-loop motif Lys residue within 5 Å of the β-phosphate. This analysis yielded 3136 complexes in 1383 structures with various substrates: ATP and GTP, their nonhydrolyzable analogues, and ADP/GDP molecules associated with γ-phosphate-mimicking moieties; see Figure 2 in the companion paper [ 30 ].…”
Section: Methodsmentioning
confidence: 99%
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