NDLI: Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase

Please wait, while we are loading the content...

Simultaneous determination of urinary cortisol, cortisone and corticosterone in parachutists, depressed patients and healthy controls in view of biomedical and pharmacokinetic studies

Contribution of gross chromosomal changes to HPV16-induced transformation

Synergistic anti-cancer effects via co-delivery of TNF-related apoptosis-inducing ligand (TRAIL/Apo2L) and doxorubicin using micellar nanoparticles

Shot-gun proteomic analysis of mitochondrial D-loop DNA binding proteins: identification of mitochondrial histones

Beyond glucose: metabolic shifts in responses to the effects of the oral glucose tolerance test and the high-fructose diet in rats

Insights into the complex biosynthesis of the leupyrrins in Sorangium cellulosum So ce690

Synthesis and evaluation of conformationally restricted inhibitors of aspartate semialdehyde dehydrogenase

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models

Impact of protein tyrosine kinase 6 (PTK6) on human epidermal growth factor receptor (HER) signalling in breast cancer

Genome-wide transcriptome and proteome analysis of Escherichia coli expressing IrrE, a global regulator of Deinococcus radiodurans

N-linked glycan changes of serum haptoglobin β chain in liver disease patients

Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes

Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase

Comparative analysis on the membrane proteome of Clostridium acetobutylicum wild type strain and its butanol-tolerant mutant

HPLC-MS aided PC12 cell systems: to quantitatively monitor the conversion of nitronyl nitroxide in biological systems with and without NO

Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection

Mapping ApoE/Aβ binding regions to guide inhibitor discovery

Redox active copper chelate overcomes multidrug resistance in T-lymphoblastic leukemia cell by triggering apoptosis

Controlling transcriptional programs for cellular adaptation by chromatin regulation

Capturing cancer cells using aptamer-immobilized square capillary channels

Nano-LC-MS/MS based proteomics of hepatocellular carcinoma cells compared to Chang liver cells and tanshinone IIA induction

DNA-based strategies for blocking HMGB1 cytokine activity: design, synthesis and preliminary in vitro/in vivo assays of DNA and DNA-like duplexes

The phenanthridine biguanides efficiently differentiate between dGdC, dAdT and rArU sequences by two independent, sensitive spectroscopic methods

Sequential ordering among multicolor fluorophores for protein labeling facility via aggregation-elimination based β-lactam probes

Synthesis, biological evaluation and supramolecular assembly of novel analogues of peptidyl nucleosides

Back cover

Molecular BioSystems Vol - 7 Issue - 4

Molecular BioSystems Vol - 7 Issue - 3

Molecular BioSystems Vol - 7 Issue - 2

Molecular BioSystems Vol -6

Molecular BioSystems Vol -5

Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

Molecular BioSystems Vol -2

Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase

Content Provider	Royal Society of Chemistry (RSC)
Author	Merli, Angelo Karuppasamy, Manikandan Vas, Mária Gráczer, Éva Weiss, Manfred S. Singh, Rajesh Kumar Závodszky, Péter
Copyright Year	2011
Abstract	The domain closure associated with the catalytic cycle is described at an atomic level, based on pairwise comparison of the X-ray structures of homodimeric Thermus thermophilus isopropylmalate dehydrogenase (IPMDH), and on their detailed molecular graphical analysis. The structures of the apo-form without substrate and in complex with the divalent metal–ion to 1.8 Å resolution, in complexes with both Mn2+ and 3-isopropylmalate (IPM), as well as with both Mn2+ and NADH, were determined at resolutions ranging from 2.0 to 2.5 Å. Single crystal microspectrophotometric measurements demonstrated the presence of a functionally competent protein conformation in the crystal grown in the presence of Mn2+ and IPM. Structural comparison of the various complexes clearly revealed the relative movement of the two domains within each subunit and allowed the identification of two hinges at the interdomain region: hinge 1 between αd and βF as well as hinge 2 between αh and βE. A detailed analysis of the atomic contacts of the conserved amino acid side-chains suggests a possible operational mechanism of these molecular hinges upon the action of the substrates. The interactions of the protein with Mn2+ and IPM are mainly responsible for the domain closure: upon binding into the cleft of the interdomain region, the substrate IPM induces a relative movement of the secondary structural elements βE, βF, βG, αd and αh. A further special feature of the conformational change is the movement of the loop bearing the amino acid Tyr139 that precedes the interacting arm of the subunit. The tyrosyl ring rotates and moves by at least 5 Å upon IPM-binding. Thereby, new hydrophobic interactions are formed above the buried isopropyl-group of IPM. Domain closure is then completed only through subunit interactions: a loop of one subunit that is inserted into the interdomain cavity of the other subunit extends the area with the hydrophobic interactions, providing an example of the cooperativity between interdomain and intersubunit interactions.
Starting Page	1646
Ending Page	1659
Page Count	14
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	7
Issue Number	5
Journal	Molecular BioSystems
DOI	10.1039/c0mb00346h
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	X-ray crystallography Thermus thermophilus NADH Carboxylic acid IPM Nicotinamide adenine dinucleotide Hydrophobe Cooperativity Biomolecular structure Single crystal Protein Catalytic cycle
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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

Structure and Mechanism of the Bifunctional CinA Enzyme from Thermus thermophilus

Crystallization and preliminary X-ray diffraction analysis of various enzyme–substrate complexes of isopropylmalate dehydrogenase from Thermus thermophilus

Crystallization and preliminary X-ray diffraction analysis of various enzyme-substrate complexes of isopropylmalate dehydrogenase from Thermus thermophilus.

Ligand-Induced Changes in the Conformation of 3-Isopropylmalate Dehydrogenase from Thermus thermophilus

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Conformational plasticity surrounding the active site of NADH oxidase from Thermus thermophilus

The Crystal Structures of Mutated 3-Isopropylmalate Dehydrogenase from Thermus thermophilus HB8 and Their Relationship to the Thermostability of the Enzyme

Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase.

Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure.

Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase

Similar Documents

Structure and Mechanism of the Bifunctional CinA Enzyme from Thermus thermophilus

Crystallization and preliminary X-ray diffraction analysis of various enzyme–substrate complexes of isopropylmalate dehydrogenase from Thermus thermophilus

Crystallization and preliminary X-ray diffraction analysis of various enzyme-substrate complexes of isopropylmalate dehydrogenase from Thermus thermophilus.

Ligand-Induced Changes in the Conformation of 3-Isopropylmalate Dehydrogenase from Thermus thermophilus

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Conformational plasticity surrounding the active site of NADH oxidase from Thermus thermophilus

The Crystal Structures of Mutated 3-Isopropylmalate Dehydrogenase from Thermus thermophilus HB8 and Their Relationship to the Thermostability of the Enzyme

Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase.

Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure.

Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase