Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit Enzyme

Davulcu, Omar; Flynn, Peter F.; Chapman, Michael S.; Skalicky, Jack J.

doi:10.1016/j.str.2009.08.014

Cited by 25 publications

(87 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In crystal structures, the loop has been fully resolved only in the presence of substrates. Consistent with disorder in the substrate-free states, NMRbased Lipari-Szabo analysis has identified inherent nanosecond dynamics in this region (22). It appears that substrates either induce an ordering or select from an ensemble of loop conformations (23-25) to achieve a substrate-bound conformation that is catalytically competent for the cognate phosphagen substrate.…”

mentioning

confidence: 82%

“…These motions, measured in the absence of substrates, occur at turnover-commensurate rates (22) at sites that are also implicated in the substrate-associated conformation changes (36). These observations suggest that substrate-associated changes take advantage of modes of flexibility intrinsic to the enzyme and that some of the intrinsic motions may be rate-limiting on turnover.…”

mentioning

confidence: 83%

“…Large Domain Specificity Loop-One of the changes induced in UcLK by nucleotide affects a loop known in LpAK to be intrinsically dynamic in the nanosecond regime (22), UcLK loop 309 -317. There are three interactions of the protein backbone with the nucleotide.…”

Section: Nucleotide Binding and Dynamic Loopsmentioning

confidence: 99%

“…In some structures, the loop points away from the active site in several configurations with active site residues up to 18 Å from their well resolved transition state locations. In one of these structures, human brain CK (HsCK BB ), the loop contains an ␣-helix (60), but NMR chemical shift shows the LpAK solution structure to be nonhelical (22). Thus, locally the substrate-free loop structure is not conserved and/or is influenced by the crystal environment.…”

Section: Nucleotide Binding and Dynamic Loopsmentioning

confidence: 99%

“…C-terminal domains and in LpAK active site loop 182-209 (corresponding to UcLK loop 175-203) (22). These motions, measured in the absence of substrates, occur at turnover-commensurate rates (22) at sites that are also implicated in the substrate-associated conformation changes (36).…”

mentioning

confidence: 99%

See 4 more Smart Citations

The Structure of Lombricine Kinase

Bush

Kirillova

Clark

et al. 2011

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309 -317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His 178 . Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.Lombricine, arginine, and creatine kinases (EC 2.7.3) are homologous phosphagen kinases that catalyze the buffering of cellular ATP levels through phosphoryl transfer to/from their respective guanidino-containing substrates. The reaction is central to short-term temporal energy buffering (1, 2) as well as in spatial shuttling of energy from production to consumption sites (3-5). A wide array of endergonic processes is driven by nucleotide hydrolysis, from motion in molecular motors, active transport, and synthetic metabolism to signal transduction. Thus, the maintenance of a constant ATP/ADP ratio, displaced far from thermodynamic equilibrium in the face of high and variable rates of ATP turnover, is crucial for cellular homeostasis (2).Different organisms use different phosphagen substrates, usually only one and each with its own specific phosphagen kinase ( Fig. 1) (2). Lombricine kinase, as well as taurocyamine kinase and glycocyamine kinase, is found exclusively in annelids and allied groups (2). Phylogenetic analyses and studies of the intron/exon organization of the genes of these phosphagen kinases unique to annelids have shown that they are more closely related to creatine kinases (with which they share 50 -60% sequence identity) than typical monomeric arginine kinases such as that from the horseshoe crab (6) (40% sequence identity). Annelids are more diverse in their choice of phosphagen, and the substrate specificities of the corresponding kinases are often lower (6).Structural work has concentrated on the presumptive ancestral arginine kinase and the vertebrate creatine kinase (7, 8), but sequence alignment suggests that subunit fold, if not quaternary structure, is conserved across the fa...

show abstract

mentioning

confidence: 82%

mentioning

confidence: 83%

Section: Nucleotide Binding and Dynamic Loopsmentioning

confidence: 99%

Section: Nucleotide Binding and Dynamic Loopsmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

The Structure of Lombricine Kinase

Bush

Kirillova

Clark

et al. 2011

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

Dynamics in Enzymes: Solution NMR Studies

Loria

2012

Encyclopedia of Magnetic Resonance

View full text Add to dashboard Cite

Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data

Hansen

Peng

et al. 2016

Angewandte Chemie

View full text Add to dashboard Cite

Functional motions of 15N‐labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG‐type experiments. CEST also simultaneously reports on site‐specific R1 and R2 parameters. It is shown here how CEST‐derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a “lean” version of the model‐free approach S2 order parameters can be determined that match those from the standard model‐free approach applied to 15N R1, R2, and {1H}‐15N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond‐to‐millisecond timescales.

show abstract

Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit Enzyme

Cited by 25 publications

References 59 publications

The Structure of Lombricine Kinase

The Structure of Lombricine Kinase

Dynamics in Enzymes: Solution NMR Studies

Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data

Contact Info

Product

Resources

About