PDBsum entry 5gij

Signaling protein

PDB id

5gij

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Contents

			Protein chains

					603 a.a.


					12 a.a.

			Ligands

					NAG-NAG-MAN


					NAG-NAG ×4


					NAG-NAG-MAN-MAN


					NAG-NAG-MAN-MAN- FUC


					NAG ×4

PDB id:

5gij

Links

Name:

Signaling protein

Title:

Crystal structure of tdr-tdif complex

Structure:

Leucine-rich repeat receptor-like protein kinase tdr. Chain: b. Fragment: extracellular domain, unp residues 31-631. Synonym: protein phloem intercalated with xylem,tracheary element differentiation inhibitory factor receptor,tdif receptor. Engineered: yes. Mutation: yes. Peptide from clavata3/esr (cle)-related protein 41. Chain: d.

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: tdr, pxy, at5g61480, mci2.4. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Synthetic: yes. Organism_taxid: 3702

Resolution:

3.00Å

R-factor:

0.218

R-free:

0.237

Authors:

J.Morita,K.Kato,R.Ishitani,H.Nishimasu,O.Nureki

Key ref:

J.Morita et al. (2016). Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide. Nat Commun, 7, 12383. PubMed id: 27498761 DOI: 10.1038/ncomms12383

Date:

23-Jun-16

Release date:

24-Aug-16

PROCHECK

	Headers

	References

Protein chain

Q9FII5 (TDR_ARATH) - Leucine-rich repeat receptor-like protein kinase TDR from Arabidopsis thaliana

Seq: Struc:

Seq: Struc:

Seq: Struc:					1041 a.a. 603 a.a.*

Protein chain

Q84W98 (CLE41_ARATH) - CLAVATA3/ESR (CLE)-related protein 41 from Arabidopsis thaliana

Seq: Struc:					99 a.a. 12 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 10 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

Chain B: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
2.	L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein]	+	ATP	=	O-phospho-L-seryl-[protein] Bound ligand (Het Group name = NAG) matches with 41.38% similarity	+	ADP	+	H(+)

L-threonyl-[protein]	+	ATP	=	O-phospho-L-threonyl-[protein] Bound ligand (Het Group name = NAG) matches with 41.38% similarity	+	ADP	+	H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/ncomms12383	Nat Commun 7:12383 (2016)
PubMed id: 27498761

Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide.
J.Morita, K.Kato, T.Nakane, Y.Kondo, H.Fukuda, H.Nishimasu, R.Ishitani, O.Nureki.

ABSTRACT

In plants, leucine-rich repeat receptor-like kinases (LRR-RKs) perceive ligands, including peptides and small molecules, to regulate various physiological processes. TDIF, a member of the CLE peptide family, specifically interacts with the LRR-RK TDR to inhibit meristem differentiation into tracheary elements, and promotes cell proliferation. Here we report the crystal structure of the extracellular domain of TDR in complex with the TDIF peptide. The extracellular domain of TDR adopts a superhelical structure comprising 22 LRRs, and specifically recognizes TDIF by its inner concave surface. Together with our biochemical and sequence analyses, our structure reveals a conserved TDIF-recognition mechanism of TDR among plant species. Furthermore, a structural comparison of TDR with other plant LRR-RKs suggested the activation mechanism of TDR by TDIF. The structure of this CLE peptide receptor provides insights into the recognition mechanism of the CLE family peptides.