NDLI: Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites

Content Provider	PubMed Central
Author	Summerton, Jean C. Martin, Gregory M. Evanseck, Jeffrey D. Chapman, Michael S.
Editor	Agarwal, Pratul K.
Copyright Year	2014
Abstract	Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3β of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3β have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3β interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM.
Related Links	http://dx.doi.org/10.1371/journal.pone.0108310
Starting Page	108310
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	9
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-09-19
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome

Identification of active sites in amidase: Evolutionary relationship between amide bond- and peptide bond-cleaving enzymes

Hydrogen bond dynamics in the active site of photoactive yellow protein

CHROMIUM (III)-NUCLEOTIDE COMPLEXES AS PARAMAGNETIC PROBES FOR CATALYTIC SITES OF PHOSPHORYL TRANSFER ENZYMES

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions

Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick

Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase

Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites

Similar Documents

Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome

Identification of active sites in amidase: Evolutionary relationship between amide bond- and peptide bond-cleaving enzymes

Hydrogen bond dynamics in the active site of photoactive yellow protein

CHROMIUM (III)-NUCLEOTIDE COMPLEXES AS PARAMAGNETIC PROBES FOR CATALYTIC SITES OF PHOSPHORYL TRANSFER ENZYMES

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions

Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick

Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase

Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites