PDBsum entry 3dm0

Sugar binding protein,signaling protein

PDB id

3dm0

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Contents

			Protein chain

					675 a.a. *

			Ligands

					GLC-GLC


					EDO

			Waters ×273

* Residue conservation analysis

PDB id:

3dm0

Links

Name:

Sugar binding protein,signaling protein

Title:

Maltose binding protein fusion with rack1 from a. Thaliana

Structure:

Maltose-binding periplasmic protein fused with rack1. Chain: a. Fragment: fusion protein of mbp (unp residues 27 to 387 ) and rack1 (unp residues 4 to 327). Engineered: yes. Mutation: yes

Source:

Escherichia coli, arabidopsis thaliana. Organism_taxid: 83333, 3702. Gene: male, b4034, jw3994,arca, at1g18080, t10f20.9, t10o22.6. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å

R-factor:

0.210

R-free:

0.250

Authors:

H.Ullah,E.L.Scappini,A.F.Moon,L.V.Williams,D.L.Armstrong,L.C.Pedersen

Key ref:

H.Ullah et al. (2008). Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana. Protein Sci, 17, 1771-1780. PubMed id: 18715992 DOI: 10.1110/ps.035121.108

Date:

30-Jun-08

Release date:

09-Sep-08

PROCHECK

	Headers

	References

Protein chain

O24456 (GBLPA_ARATH) - Small ribosomal subunit protein RACK1z from Arabidopsis thaliana

Seq: Struc:

Seq: Struc:					327 a.a. 675 a.a.*

Protein chain

P0AEX9 (MALE_ECOLI) - Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: Struc:

Seq: Struc:					396 a.a. 675 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 12 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.?

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

DOI no: 10.1110/ps.035121.108	Protein Sci 17:1771-1780 (2008)
PubMed id: 18715992

Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana.
H.Ullah, E.L.Scappini, A.F.Moon, L.V.Williams, D.L.Armstrong, L.C.Pedersen.

ABSTRACT

The receptor for activated C-kinase 1 (RACK1) is a highly conserved WD40 repeat scaffold protein found in a wide range of eukaryotic species from Chlamydymonas to plants and humans. In tissues of higher mammals, RACK1 is ubiquitously expressed and has been implicated in diverse signaling pathways involving neuropathology, cellular stress, protein translation, and developmental processes. RACK1 has established itself as a scaffold protein through physical interaction with a myriad of signaling proteins ranging from kinases, phosphatases, ion channels, membrane receptors, G proteins, IP3 receptor, and with widely conserved structural proteins associated with the ribosome. In the plant Arabidopsis thaliana, RACK1A is implicated in diverse developmental and environmental stress pathways. Despite the functional conservation of RACK1-mediated protein-protein interaction-regulated signaling modes, the structural basis of such interactions is largely unknown. Here we present the first crystal structure of a RACK1 protein, RACK1 isoform A from Arabidopsis thaliana, at 2.4 A resolution, as a C-terminal fusion of the maltose binding protein. The structure implicates highly conserved surface residues that could play critical roles in protein-protein interactions and reveals the surface location of proposed post-transcriptionally modified residues. The availability of this structure provides a structural basis for dissecting RACK1-mediated cellular signaling mechanisms in both plants and animals.

Selected figure(s)



	Figure 2. Figure 2. Ribbon diagram of Asp–His–Ser hydrogen-bonding network responsible for maintaining the integrity of the β-sheet within blade 2 of the β-propeller. His62 lies on the loop connecting blade 1 with blade 2. Trp90 and Asp91 represent the WD repeat of blade 2.		Figure 4. Figure 4. Surface diagrams of conserved regions within the RACK1 proteins. (A) Conserved region 1. Conserved residues are colored according to the blade to which they belong based on the ribbon diagram in Figure 1B. Residues Arg36, Trp83, Arg125, Trp152, and Lys214 line the upper rim of the β-propeller pore. (B) Conserved region 2. Tyr230 and Tyr248 on RACK1A are proposed phosphorylation sites. Residue Pro204 is located on the lower rim of the pore of the β-propeller. Molecular surfaces were created using PyMOL (DeLano Scientific).

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21272581

A.Gómez-Arreaza, H.Acosta, X.Barros-Álvarez, J.L.Concepción, F.Albericio, and L.Avilan (2011).
Leishmania mexicana: LACK (Leishmania homolog of receptors for activated C-kinase) is a plasminogen binding protein.

Exp Parasitol, 127, 752-761.

21098678

J.Guo, S.Wang, O.Valerius, H.Hall, Q.Zeng, J.F.Li, D.J.Weston, B.E.Ellis, and J.G.Chen (2011).
Involvement of Arabidopsis RACK1 in protein translation and its regulation by abscisic acid.

Plant Physiol, 155, 370-383.

21280218

N.V.Bykova, B.Hoehn, C.Rampitsch, T.Banks, J.A.Stebbing, T.Fan, and R.Knox (2011).
Redox-sensitive proteome and antioxidant strategies in wheat seed dormancy control.

Proteomics, 11, 865-882.

21460442

Z.S.Derewenda (2011).
It's all in the crystals….

Acta Crystallogr D Biol Crystallogr, 67, 243-248.

20226507

G.A.Mueller, L.L.Edwards, J.J.Aloor, M.B.Fessler, J.Glesner, A.Pomés, M.D.Chapman, R.E.London, and L.C.Pedersen (2010).
The structure of the dust mite allergen Der p 7 reveals similarities to innate immune proteins.

J Allergy Clin Immunol, 125, 909.

PDB code:

3h4z

20529362

K.A.Gonçalves, J.C.Borges, J.C.Silva, P.F.Papa, G.C.Bressan, I.L.Torriani, and J.Kobarg (2010).
Solution structure of the human signaling protein RACK1.

BMC Struct Biol, 10, 15.

20445236

Z.S.Derewenda (2010).
Application of protein engineering to enhance crystallizability and improve crystal properties.

Acta Crystallogr D Biol Crystallogr, 66, 604-615.

20004163

D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.

Structure, 17, 1591-1604.

PDB codes:

3jyv 3jyw 3jyx

19552624

H.W.Xue, X.Chen, and Y.Mei (2009).
Function and regulation of phospholipid signalling in plants.

Biochem J, 421, 145-156.

19584117

J.Guo, J.Wang, L.Xi, W.D.Huang, J.Liang, and J.G.Chen (2009).
RACK1 is a negative regulator of ABA responses in Arabidopsis.

J Exp Bot, 60, 3819-3833.

19651700

J.Guo, S.Wang, J.Wang, W.D.Huang, J.Liang, and J.G.Chen (2009).
Dissection of the relationship between RACK1 and heterotrimeric G-proteins in Arabidopsis.

Plant Cell Physiol, 50, 1681-1694.

19941347

M.F.Oginsky, E.W.Rodgers, M.C.Clark, R.Simmons, W.D.Krenz, and D.J.Baro (2009).
D(2) receptors receive paracrine neurotransmission and are consistently targeted to a subset of synaptic structures in an identified neuron of the crustacean stomatogastric nervous system.

J Comp Neurol, 518, 255-276.

19423701

P.A.Kiely, G.S.Baillie, R.Barrett, D.A.Buckley, D.R.Adams, M.D.Houslay, and R.O'Connor (2009).
Phosphorylation of RACK1 on tyrosine 52 by c-Abl is required for insulin-like growth factor I-mediated regulation of focal adhesion kinase.

J Biol Chem, 284, 20263-20274.

19114558

S.M.Coyle, W.V.Gilbert, and J.A.Doudna (2009).
Direct link between RACK1 function and localization at the ribosome in vivo.

Mol Cell Biol, 29, 1626-1634.

PDB code:

3frx

19674157

Y.Ikebuchi, T.Takada, K.Ito, T.Yoshikado, N.Anzai, Y.Kanai, and H.Suzuki (2009).
Receptor for activated C-kinase 1 regulates the cellular localization and function of ABCB4.

Hepatol Res, 39, 1091-1107.

18947417

J.Guo, and J.G.Chen (2008).
RACK1 genes regulate plant development with unequal genetic redundancy in Arabidopsis.

BMC Plant Biol, 8, 108.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.