PDBsum entry 5wfn

Motor protein

PDB id: 5wfn

Contents

Protein chains

370 a.a.

193 a.a.

Ligands

ANP ×2

Metals

_MG ×2

PDB id:

5wfn

Name:

Motor protein

Title:

Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4rwt)

Structure:

Actin-5c. Chain: a, b. Engineered: yes. Mutation: yes. Leiomodin-2. Chain: c, d. Synonym: cardiac leiomodin, c-lmod, leiomodin. Engineered: yes. Mutation: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: act5c, cg4027. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Homo sapiens. Human. Organism_taxid: 9606.

Resolution:

3.00Å R-factor: 0.210 R-free: 0.246

Authors:

Z.Yurtsever,M.J.Eck,R.Dominguez

Key ref:

M.Boczkowska et al. (2017). Crystal Structure of Leiomodin 2 in Complex with Actin: A Structural and Functional Reexamination. Biophys J, 113, 889-899. PubMed id: 28834725

Date:

12-Jul-17 Release date: 30-Aug-17

Protein chains

P10987  (ACT1_DROME) -  Actin-5C from Drosophila melanogaster

Seq: 376 a.a.

Struc: 370 a.a.*

Protein chains

Q6P5Q4  (LMOD2_HUMAN) -  Leiomodin-2 from Homo sapiens

Seq: 547 a.a.

Struc: 193 a.a.*

* PDB and UniProt seqs differ at 25 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.3.6.4.- - ?????
• Enzyme class 3: Chains C, D: E.C.?

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.

Biophys J 113:889-899 (2017)

PubMed id: 28834725

Crystal Structure of Leiomodin 2 in Complex with Actin: A Structural and Functional Reexamination.

M.Boczkowska, Z.Yurtsever, G.Rebowski, M.J.Eck, R.Dominguez.

ABSTRACT

Leiomodins (Lmods) are a family of actin filament nucleators related to tropomodulins (Tmods), which are pointed end-capping proteins. Whereas Tmods have alternating tropomyosin- and actin-binding sites (TMBS1, ABS1, TMBS2, ABS2), Lmods lack TMBS2 and half of ABS1, and present a C-terminal extension containing a proline-rich domain and an actin-binding Wiskott-Aldrich syndrome protein homology 2 (WH2) domain that is absent in Tmods. Most of the nucleation activity of Lmods resides within a fragment encompassing ABS2 and the C-terminal extension. This fragment recruits actin monomers into a polymerization nucleus. Here, we revise a recently reported structure of this region of Lmod2 in complex with actin and provide biochemical validation for the newly revised structure. We find that instead of two actin subunits connected by a single Lmod2 polypeptide, as reported in the original structure, the P1 unit cell contains two nearly identical copies of actin monomers, each bound to Lmod2's ABS2 and WH2 domain, with no electron density connecting these two domains. Moreover, we show that the two actin molecules in the unit cell are related to each other by a local twofold noncrystallographic symmetry axis, a conformation clearly distinct from that of actin subunits in the helical filament. We further find that a proposed actin-binding site within the missing connecting region of Lmod2, termed helix h1, does not bind actin in vitro and that the electron density assigned to it in the original structure corresponds instead to a WH2 domain with opposite backbone directionality. Polymerization assays using Lmod2 mutants of helix h1 and the WH2 domain support this conclusion. Finally, we find that deleting the C-terminal extension of Lmod1 and Lmod2 results in an approximately threefold decrease in the nucleation activity, which is only partially accounted for by the lack of the WH2 domain.