3ZIE | pdb_00003zie

SepF-like protein from Archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb3ZIE/pdb

Classification: CELL CYCLE
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-01-08 Released: 2013-11-20
Deposition Author(s): Duman, R., Ishikawa, S., Celik, I., Ogasawara, N., Lowe, J., Hamoen, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.244 (Depositor), 0.185 (DCC)
R-Value Work:
0.188 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and Genetic Analyses Reveal the Protein Sepf as a New Membrane Anchor for the Z Ring

Duman, R., Ishikawa, S., Celik, I., Strahl, H., Ogasawara, N., Troc, P., Lowe, J., Hamoen, L.W.

(2013) Proc Natl Acad Sci U S A 110: E4601

PubMed: 24218584 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1313978110
Primary Citation Related Structures:
3ZIE, 3ZIG, 3ZIH, 3ZII

PubMed Abstract:
A key step in bacterial cell division is the polymerization of the tubulin homolog FtsZ at midcell. FtsZ polymers are anchored to the cell membrane by FtsA and are required for the assembly of all other cell division proteins. In Gram-positive and cyanobacteria, FtsZ filaments are aligned by the protein SepF, which in vitro polymerizes into large rings that bundle FtsZ filaments. Here we describe the crystal structure of the only globular domain of SepF, located within the C-terminal region. Two-hybrid data revealed that this domain comprises the FtsZ binding site, and EM analyses showed that it is sufficient for ring formation, which is explained by the filaments in the crystals of SepF. Site-directed mutagenesis, gel filtration, and analytical ultracentrifugation indicated that dimers form the basic units of SepF filaments. High-resolution structured illumination microscopy suggested that SepF is membrane associated, and it turned out that purified SepF not only binds to lipid membranes, but also recruits FtsZ. Further genetic and biochemical analyses showed that an amphipathic helix at the N terminus functions as the membrane-binding domain, making SepF a unique membrane anchor for the FtsZ ring. This clarifies why Bacillus subtilis grows without FtsA or the putative membrane anchor EzrA and why bacteria lacking FtsA contain SepF homologs. Both FtsA and SepF use an amphipathic helix for membrane binding. These helices prefer positively curved membranes due to relaxed lipid density; therefore this type of membrane anchor may assist in keeping the Z ring positioned at the strongly curved leading edge of the developing septum.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

Macromolecule Content

Total Structure Weight: 58.54 kDa
Atom Count: 4,331
Modeled Residue Count: 500
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEPF-LIKE PROTEIN	A, B, C, D, E A, B, C, D, E, F	86	Archaeoglobus fulgidus	Mutation(s): 1
UniProt
Find proteins for O29476 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29476 Go to UniProtKB: O29476
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29476
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244 (Depositor), 0.185 (DCC)
R-Value Work: 0.188 (Depositor), 0.194 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.02	α = 90
b = 64.09	β = 90
c = 82.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2013-12-11
Changes: Database references
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary