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J Biol Chem. 2019 Jan 4;294(1):142-156. doi: 10.1074/jbc.RA118.003956. Epub 2018 Nov 13.

Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat.

Author information

1
From the State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
2
the School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China.
3
the University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France, stephane.rety@ens-lyon.fr.
4
the Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China, and.
5
From the State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China, xxi01@ens-cachan.fr.
6
the LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61 Avenue du Président Wilson, F-94235 Cachan, France.

Abstract

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.

KEYWORDS:

LBD proteins; LOB domain; TtRa2LD; cooperative binding; molecular model; plant molecular biology; small-angle X-ray scattering (SAXS); structural biology; transcription factor; zinc finger

PMID:
30425099
PMCID:
PMC6322873
[Available on 2020-01-04]
DOI:
10.1074/jbc.RA118.003956
[Indexed for MEDLINE]

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