5LY0 | pdb_00005ly0

Crystal structure of LOB domain of Ramosa2 from Wheat

PDB DOI: https://doi.org/10.2210/pdb5LY0/pdb

Classification: TRANSCRIPTION
Organism(s): Triticum turgidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-23 Released: 2017-10-25
Deposition Author(s): Wei, X.-B., Zhang, B., Chen, W.-F., Fan, S.-H., Rety, S., Xi, X.-G.
Funding Organization(s): National Natural Science Foundation, Northwest A University Startup Funding

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.231 (Depositor), 0.238 (DCC)
R-Value Work:
0.201 (Depositor), 0.211 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

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

Chen, W.F., Wei, X.B., Rety, S., Huang, L.Y., Liu, N.N., Dou, S.X., Xi, X.G.

(2019) J Biological Chem 294: 142-156

PubMed: 30425099 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.RA118.003956
Primary Citation Related Structures:
5LY0

PubMed 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.

Organizational Affiliation

State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.

Macromolecule Content

Total Structure Weight: 28.21 kDa
Atom Count: 1,811
Modeled Residue Count: 215
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LOB family transfactor Ramosa2.1	A, B	131	Triticum turgidum	Mutation(s): 0
UniProt
Find proteins for D9MPF3 (Triticum turgidum subsp. durum) Explore D9MPF3 Go to UniProtKB: D9MPF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9MPF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]