PDBsum entry 3d6t

Transferase

PDB id: 3d6t

Contents

Protein chain

125 a.a. *

Ligands

GDP

Metals

_MG

Waters ×6

* Residue conservation analysis

PDB id:

3d6t

Name:

Transferase

Title:

Structure of the roc domain from the parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric gtpase

Structure:

Leucine-rich repeat serine/threonine-protein kinase 2. Chain: b. Fragment: miro domain. Synonym: dardarin. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: lrrk2, park8. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.43Å R-factor: 0.216 R-free: 0.307

Authors:

J.Deng

Key ref:

J.Deng et al. (2008). Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase. Proc Natl Acad Sci U S A, 105, 1499-1504. PubMed id: 18230735 DOI: 10.1073/pnas.0709098105

Date:

20-May-08 Release date: 10-Jun-08

Protein chain

Q5S007  (LRRK2_HUMAN) -  Leucine-rich repeat serine/threonine-protein kinase 2 from Homo sapiens

Seq: 2527 a.a.

Struc: 125 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• 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 = GDP) matches with 96.43% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = GDP) matches with 96.43% similarity) + ADP + H(+)

• Enzyme class 3: E.C.3.6.5.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1073/pnas.0709098105

Proc Natl Acad Sci U S A 105:1499-1504 (2008)

PubMed id: 18230735

Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase.

J.Deng, P.A.Lewis, E.Greggio, E.Sluch, A.Beilina, M.R.Cookson.

ABSTRACT

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of Parkinson's disease (PD). LRRK2 contains a Ras of complex proteins (ROC) domain that may act as a GTPase to regulate its protein kinase activity. The structure of ROC and the mechanism(s) by which it regulates kinase activity are not known. Here, we report the crystal structure of the LRRK2 ROC domain in complex with GDP-Mg(2+) at 2.0-A resolution. The structure displays a dimeric fold generated by extensive domain-swapping, resulting in a pair of active sites constructed with essential functional groups contributed from both monomers. Two PD-associated pathogenic residues, R1441 and I1371, are located at the interface of two monomers and provide exquisite interactions to stabilize the ROC dimer. The structure demonstrates that loss of stabilizing forces in the ROC dimer is likely related to decreased GTPase activity resulting from mutations at these sites. Our data suggest that the ROC domain may regulate LRRK2 kinase activity as a dimer, possibly via the C-terminal of ROC (COR) domain as a molecular hinge. The structure of the LRRK2 ROC domain also represents a signature from a previously undescribed class of GTPases from complex proteins and results may provide a unique molecular target for therapeutics in PD.

Selected figure(s)

Figure 1.
The unique dimeric ROC GTPase. (A) Stereoview of the domain-swapped dimer. The two individual monomers are shown in yellow and green. The GDP-Mg^2+ ligands are shown in ball-and-stick format. (B) Ribbon representation of a single monomer. The three head, neck, and body subdomains are indicated, along with the labeled secondary structures. The P-loop, G3/Switch II, and G4 and G5 loops are indicated in orange, pink, red, and cyan, respectively. The disordered G2 loop is shown as a black dotted curve. (C) Surface representation highlighting the GDP-Mg^2+ binding pocket on the surface of the dimer that is contributed from both monomers. The pair of functional units are shown as ROCs1 and ROCs2, respectively.

Figure 2.
Structural basis of PD-associated mutations in ROC. (A) R1441 and W1434 from one monomer together with F1401 and P1406 from the other stack on each other alternately, forming a hydrophobic zipper at the dimer interface. The guanidinium group of R1441 also is hydrogen-bonded with the backbone carbonyl oxygen of F1401 and the hydroxyl group of T1404 on helix α2 from the other peptide chain. 2mF [o] − DF [c] electron density map is shown in blue. (B) I1371 is inserted in a hydrophobic cavity, which is constructed by residues from both monomers at the dimer interface. I1371 is shown in stick format and colored in orange. The surrounding residues are shown in stick format within the semitransparent surface representation. The color scheme is the same as that in Fig. 1. Note the side-chain methyl group of T1404 is pointing directly to the tip of I1371, forming a favorable van der Waals' interaction. (C) R1441C (lane 3), as a prototypical mutation at the dimer interface, decreases interaction with the full-length wild-type LRRK2 protein compared with wild-type GST fusions (lane 2); no interaction was seen with GST alone (lane 1). (D) Pull-down assays were quantified and corrected for the amount of LRRK2 protein in the inputs (middle blots). *, P < 0.0001; **, P < 0.01 compared with GST alone (one-way ANOVA with Student–Newman–Kuell's post hoc test; n = 3).

Figures were selected by the author.