PDBsum entry 2bot

Contractile protein

PDB id: 2bot

Contents

Protein chains

100 a.a.

100 a.a.

Theoretical model

PDB id:

2bot

Name:

Contractile protein

Title:

Homology-based model of the dynein coiled-coil stalk in the 22:19 configuration.

Structure:

Dynein heavy chain. Synonym: dyhc, cytoplasmic dynein heavy chain 1, dyhc1. Chain: a. Fragment: stalk, residues 3197-3296. Dynein heavy chain. Synonym: dyhc, cytoplasmic dynein heavy chain 1, dyhc1. Chain: b. Fragment: stalk, residues 3398-3497

Source:

Homo sapiens. Human. Human

Authors:

I.R.Gibbons,J.E.Garbarino,C.E.Tan,S.L.Reck-Peterson, R.D.Vale,A.P.Carter

Key ref:

I.R.Gibbons et al. (2005). The affinity of the dynein microtubule-binding domain is modulated by the conformation of its coiled-coil stalk. J Biol Chem, 280, 23960-23965. PubMed id: 15826937 DOI: 10.1074/jbc.M501636200

Date:

13-Apr-05 Release date: 18-Apr-05

Protein chain

Q14204  (DYHC1_HUMAN) -  Cytoplasmic dynein 1 heavy chain 1 from Homo sapiens

Seq: 4646 a.a.

Struc: 100 a.a.

Protein chain

Q14204  (DYHC1_HUMAN) -  Cytoplasmic dynein 1 heavy chain 1 from Homo sapiens

Seq: 4646 a.a.

Struc: 100 a.a.

DOI no: 10.1074/jbc.M501636200

J Biol Chem 280:23960-23965 (2005)

PubMed id: 15826937

The affinity of the dynein microtubule-binding domain is modulated by the conformation of its coiled-coil stalk.

I.R.Gibbons, J.E.Garbarino, C.E.Tan, S.L.Reck-Peterson, R.D.Vale, A.P.Carter.

ABSTRACT

The microtubule-binding domain (MTBD) of dynein is separated from the AAA (ATPase with any other activity) core of the motor by an approximately 15-nm stalk that is predicted to consist of an antiparallel coiled coil. However, the structure of this coiled coil and the mechanism it uses to mediate communication between the MTBD and ATP-binding core are unknown. Here, we sought to identify the optimal alignment between the hydrophobic heptad repeats in the two strands of the stalk coiled coil. To do this, we fused the MTBD of mouse cytoplasmic dynein, together with 12-36 residues of its stalk, onto a stable coiled-coil base provided by Thermus thermophilus seryl-tRNA synthetase and tested these chimeric constructs for microtubule binding in vitro. The results identified one alignment that yielded a protein displaying high affinity for microtubules (2.2 microM). The effects of mutations applied to the MTBD of this construct paralleled those previously reported (Koonce, M. P., and Tikhonenko, I. (2000) Mol. Biol. Cell 11, 523-529) for an intact dynein motor unit in the absence of ATP, suggesting that it resembles the tight binding state of native intact dynein. All other alignments showed at least 10-fold lower affinity for microtubules with the exception of one, which had an intermediate affinity. Based on these results and on amino acid sequence analysis, we hypothesize that dynein utilizes small amounts of sliding displacement between the two strands of its coiled-coil stalk as a means of communication between the AAA core of the motor and the MTBD during the mechanochemical cycle.

Selected figure(s)

Figure 1.
FIG. 1. Molecular structure of intact cytoplasmic dynein. The cytoplasmic dynein motor is a dimer containing two identical heavy chain subunits of molecular mass 520 kDa. The core of the motor, formed by the C-terminal two-thirds of the heavy chain, comprises a ring of six AAA ATPase domains, depicted here in blue and purple. The MTBD (blue) protrudes from the AAA core on a coiled-coil stalk (gray). The attachment of cargo to the dynein motor involves light and intermediate chain subunits (green) that are associated with the N-terminal third of the heavy chain. This figure was adapted from Ref. 2 with permission.

Figure 5.
FIG. 5. Structural models of the dynein stalk. A, models of a section of the dynein stalk in configurations expected to correspond to those occurring in SRS-22:19 or SRS19:19. CC2 is shown in surface representation with hydrophobic residues (Val, Ile, Leu, Ala, Met, Tyr) in the coiled-coil core ("a" and "d" positions) colored green. CC1 is shown in backbone representation (gray) with side chains included for Ser-3224 (yellow), Leu-3227 (cyan; with asterisk) and Lys-3230 (magenta). In passing from the configuration of SRS-22:19 to that of SRS-19:19, the side chain of Leu-3227 shifts from packing against one side of CC2 (left) to packing against the other side (right), potentially by following the hydrophobic-lined groove formed by Ile-3459, Leu-3463, Val-3466 and Val-3470 in the surface of CC2 (dashed line). Similar hydrophobic grooves in the core interface of CC2 occur in most other heptads along the length of the stalk coiled coil (supplemental material). B, schematics depicting transverse sections through the coiled-coil stalk in the region shown in A. Residues in CC1 are colored as in A to illustrate that Leu-3227 (cyan) shifts from a "d" heptad position to an "a" position in going between the 22:19 and 19:19 configurations (see also Fig. 2A). Panel A of this figure was prepared with the program MOLMOL (22). Coordinates of these models have been deposited in the theoretical models section of the Protein Data Bank under the identifiers 2BOT (SRS-22:19) and 2BOR (SRS-19:19).

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2005, 280, 23960-23965) copyright 2005.

Figures were selected by an automated process.