Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.87 kDa 
• Atom Count: 2213 
• Modelled Residue Count: 284 
• Deposited Residue Count: 296 
• Unique protein chains: 1

5LPB

Crystal structure of the BRI1 kinase domain (865-1160) in complex with ADP from Arabidopsis thaliana

• PDB DOI: 10.2210/pdb5LPB/pdb
• Entry: 5LPB supersedes: 4OAC

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-12 Released: 2016-08-31 
• Deposition Author(s): Bojar, D., Martinez, J., Hothorn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.203 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation.

Bojar, D., Martinez, J., Santiago, J., Rybin, V., Bayliss, R., Hothorn, M.

(2014) Plant J 78: 31-43

• PubMed: 24461462 
• DOI: 10.1111/tpj.12445
• Primary Citation of Related Structures:  
  5LPB, 5LPW, 5LPZ


• PubMed Abstract: 
  

Brassinosteroids, which control plant growth and development, are sensed by the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1). Brassinosteroid binding to the BRI1 leucine-rich repeat (LRR) domain induces heteromerisation with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK)-family co-receptor. This process allows the cytoplasmic kinase domains of BRI1 and SERK to interact, trans-phosphorylate and activate each other. Here we report crystal structures of the BRI1 kinase domain in its activated form and in complex with nucleotides. BRI1 has structural features reminiscent of both serine/threonine and tyrosine kinases, providing insight into the evolution of dual-specificity kinases in plants. Phosphorylation of Thr1039, Ser1042 and Ser1044 causes formation of a catalytically competent activation loop. Mapping previously identified serine/threonine and tyrosine phosphorylation sites onto the structure, we analyse their contribution to brassinosteroid signaling. The location of known genetic missense alleles provide detailed insight into the BRI1 kinase mechanism, while our analyses are inconsistent with a previously reported guanylate cyclase activity. We identify a protein interaction surface on the C-terminal lobe of the kinase and demonstrate that the isolated BRI1, SERK2 and SERK3 cytoplasmic segments form homodimers in solution and have a weak tendency to heteromerise. We propose a model in which heterodimerisation of the BRI1 and SERK ectodomains brings their cytoplasmic kinase domains in a catalytically competent arrangement, an interaction that can be modulated by the BRI1 inhibitor protein BKI1.

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Organizational Affiliation: 

Structural Plant Biology Lab, Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076, Tuebingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A	296	Arabidopsis thaliana	Mutation(s): 1  Gene Names: BRI1, At4g39400, F23K16.30 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for O22476 (Arabidopsis thaliana) Explore O22476  Go to UniProtKB:  O22476

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.203 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.141	α = 90
b = 116.141	β = 90
c = 49.743	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-12 
• Released Date: 2016-08-31 
Deposition Author(s): Bojar, D., Martinez, J., Hothorn, M.
• This entry supersedes: 4OAC

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release