Abstract
Arginine kinase catalyzes reversible phosphoryl transfer between ATP and arginine, buffering cellular ATP concentrations. Structures of substrate-free and -bound enzyme have highlighted a range of conformational changes thought to occur during the catalytic cycle. Here, NMR is used to characterize the intrinsic backbone dynamics over multiple timescales. Relaxation dispersion indicates rigid-body motion of the N-terminal domain and flexible dynamics in the I182-G209 loop, both at millisecond rates commensurate with kcat, implying that either might be rate limiting upon catalysis. Lipari-Szabo analysis indicates backbone flexibility on the nanosecond timescale in the V308-V322 loop, while the rest of the enzyme is more rigid in this timescale. Thus, intrinsic dynamics are most prominent in regions that have been independently implicated in conformational changes. Substrate-free enzyme may sample an ensemble of different conformations, of which a subset is selected upon substrate binding, with critical active site residues appropriately configured for binding and catalysis.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1356-1367 |
| Number of pages | 12 |
| Journal | Structure |
| Volume | 17 |
| Issue number | 10 |
| DOIs | |
| State | Published - Oct 14 2009 |
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Keywords
- PROTEINS
ASJC Scopus subject areas
- Molecular Biology
- Structural Biology
Cite this
Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit Enzyme. / Davulcu, Omar; Flynn, Peter F.; Chapman, Michael; Skalicky, Jack J.
In: Structure, Vol. 17, No. 10, 14.10.2009, p. 1356-1367.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit Enzyme
AU - Davulcu, Omar
AU - Flynn, Peter F.
AU - Chapman, Michael
AU - Skalicky, Jack J.
PY - 2009/10/14
Y1 - 2009/10/14
N2 - Arginine kinase catalyzes reversible phosphoryl transfer between ATP and arginine, buffering cellular ATP concentrations. Structures of substrate-free and -bound enzyme have highlighted a range of conformational changes thought to occur during the catalytic cycle. Here, NMR is used to characterize the intrinsic backbone dynamics over multiple timescales. Relaxation dispersion indicates rigid-body motion of the N-terminal domain and flexible dynamics in the I182-G209 loop, both at millisecond rates commensurate with kcat, implying that either might be rate limiting upon catalysis. Lipari-Szabo analysis indicates backbone flexibility on the nanosecond timescale in the V308-V322 loop, while the rest of the enzyme is more rigid in this timescale. Thus, intrinsic dynamics are most prominent in regions that have been independently implicated in conformational changes. Substrate-free enzyme may sample an ensemble of different conformations, of which a subset is selected upon substrate binding, with critical active site residues appropriately configured for binding and catalysis.
AB - Arginine kinase catalyzes reversible phosphoryl transfer between ATP and arginine, buffering cellular ATP concentrations. Structures of substrate-free and -bound enzyme have highlighted a range of conformational changes thought to occur during the catalytic cycle. Here, NMR is used to characterize the intrinsic backbone dynamics over multiple timescales. Relaxation dispersion indicates rigid-body motion of the N-terminal domain and flexible dynamics in the I182-G209 loop, both at millisecond rates commensurate with kcat, implying that either might be rate limiting upon catalysis. Lipari-Szabo analysis indicates backbone flexibility on the nanosecond timescale in the V308-V322 loop, while the rest of the enzyme is more rigid in this timescale. Thus, intrinsic dynamics are most prominent in regions that have been independently implicated in conformational changes. Substrate-free enzyme may sample an ensemble of different conformations, of which a subset is selected upon substrate binding, with critical active site residues appropriately configured for binding and catalysis.
KW - PROTEINS
UR - http://www.scopus.com/inward/record.url?scp=70349907099&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70349907099&partnerID=8YFLogxK
U2 - 10.1016/j.str.2009.08.014
DO - 10.1016/j.str.2009.08.014
M3 - Article
C2 - 19836335
AN - SCOPUS:70349907099
VL - 17
SP - 1356
EP - 1367
JO - Structure with Folding & design
JF - Structure with Folding & design
SN - 0969-2126
IS - 10
ER -