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Please use this identifier to cite or link to this item: http://repository.iitr.ac.in/handle/123456789/26943
Title: Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin
Authors: Mukhi N.
Dhindwal S.
Uppal S.
Kapoor A.
Arya R.
Kumar, Pravindra R.Manish
Kaur J.
Kundu S.
Published in: Biochemistry
Abstract: Plant hemoglobins constitute three distinct groups: symbiotic, nonsymbiotic, and truncated hemoglobins. Structural investigation of symbiotic and nonsymbiotic (class I) hemoglobins revealed the presence of a vertebrate-like 3/3 globin fold in these proteins. In contrast, plant truncated hemoglobins are similar to bacterial truncated hemoglobins with a putative 2/2 α-helical globin fold. While multiple structures have been reported for plant hemoglobins of the first two categories, for plant truncated globins only one structure has been reported of late. Here, we report yet another crystal structure of the truncated hemoglobin from Arabidopsis thaliana (AHb3) with two water molecules in the heme pocket, of which one is distinctly coordinated to the heme iron, unlike the only available crystal structure of AHb3 with a hydroxyl ligand. AHb3 was monomeric in its crystallographic asymmetric unit; however, dimer was evident in the crystallographic symmetry, and the globin indeed existed as a stable dimer in solution. The tertiary structure of the protein exhibited a bacterial-like 2/2 α-helical globin fold with an additional N-terminal α-helical extension and disordered C-termini. To address the role of these extended termini in AHb3, which is yet unknown, N- and C-terminal deletion mutants were created and characterized and molecular dynamics simulations performed. The C-terminal deletion had an insignificant effect on most properties but perturbed the dimeric equilibrium of AHb3 and significantly influenced azide binding kinetics in the ferric state. These results along with the disordered nature of the C-terminus indicated its putative role in intramolecular or intermolecular interactions probably regulating protein-ligand and protein-protein interactions. While the N-terminal deletion did not change the overall globin fold, stability, or ligand binding kinetics, it seemed to have influenced coordination at the heme iron, the hydration status of the active site, and the quaternary structure of AHb3. Evidence indicated that the N-terminus is the predominant factor regulating the quaternary interaction appropriate to physiological requirements, dynamics of the side chains in the heme pocket, and tunnel organization in the protein matrix. © 2016 American Chemical Society.
Citation: Biochemistry, 55(12): 1724-1740
URI: https://doi.org/10.1021/acs.biochem.5b01013
http://repository.iitr.ac.in/handle/123456789/26943
Issue Date: 2016
Publisher: American Chemical Society
Keywords: Bins
Crystal structure
Dimers
Ligands
Molecular dynamics
Molecules
Porphyrins
Proteins
Arabidopsis thaliana
Crystallographic symmetry
Intermolecular interactions
Molecular dynamics simulations
Protein-protein interactions
Quaternary interactions
Structural investigation
Truncated hemoglobins
Hemoglobin
azide
dimer
globin
heme
heme iron
hydroxyl group
protein AHb3
truncated hemoglobin
unclassified drug
water
truncated hemoglobin
vegetable protein
alpha helix
amino terminal sequence
Arabidopsis thaliana
Article
binding kinetics
carboxy terminal sequence
controlled study
crystal structure
crystallography
deletion mutant
ligand binding
molecular dynamics
molecular interaction
nonhuman
priority journal
protein function
protein protein interaction
protein quaternary structure
protein structure
protein tertiary structure
Arabidopsis
chemistry
physiology
protein secondary structure
X ray crystallography
Arabidopsis
Crystallography, X-Ray
Plant Proteins
Protein Structure, Secondary
Protein Structure, Tertiary
Truncated Hemoglobins
ISSN: 62960
Author Scopus IDs: 55630780900
36082537700
35082765800
54397073700
56844886500
55064809000
13610600400
7201407194
Author Affiliations: Mukhi, N., Department of Genetics, University of Delhi, South Campus, New Delhi, 110021, India
Dhindwal, S., Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
Uppal, S., Department of Biochemistry, University of Delhi, South Campus, New Delhi, 110021, India
Kapoor, A., Department of Biochemistry, University of Delhi, South Campus, New Delhi, 110021, India
Arya, R., Department of Biochemistry, University of Delhi, South Campus, New Delhi, 110021, India
Kumar, P., Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
Kaur, J., Department of Genetics, University of Delhi, South Campus, New Delhi, 110021, India
Kundu, S., Department of Biochemistry, University of Delhi, South Campus, New Delhi, 110021, India
Funding Details: Financial aid from the University of Delhi and the Department of Science and Technology, Government of India, under the PURSE program [Dean(R)/2009/868] (J.K. and S.K.) is acknowledged. The University of Delhi is duly acknowledged for R&D funding (DRCH/R&D/2013-14/4155) (J.K. and S.K.). Fellowship support from UGC, Government of India, to N.M. and R.A. and CSIR, Government of India, to S.U. are also appreciated. Department of Science and Technology, Ministry of Science and Technology, India, डीएसटी: DRCH/R&D/2013-14/4155, R)/2009/868; Council of Scientific and Industrial Research, India, CSIR; University Grants Committee, UGC; University of Delhi, DU
Corresponding Author: Kaur, J.; Department of Genetics, India; email: jagreet@south.du.ac.in
Appears in Collections:Journal Publications [BT]

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