PDBsum entry 2z7e

Biosynthetic protein

PDB id: 2z7e

Contents

Protein chains

139 a.a. *

Ligands

SO4 ×4

FES

Waters ×162

* Residue conservation analysis

PDB id:

2z7e

Name:

Biosynthetic protein

Title:

Crystal structure of aquifex aeolicus iscu with bound [2fe-2s] cluster

Structure:

Nifu-like protein. Chain: a, b, c. Synonym: iscu protein. Engineered: yes. Mutation: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Strain: vf5. Gene: aq_896. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.225 R-free: 0.252

Authors:

Y.Shimomura,K.Wada,Y.Takahashi,K.Fukuyama

Key ref:

Y.Shimomura et al. (2008). The asymmetric trimeric architecture of [2Fe-2S] IscU: implications for its scaffolding during iron-sulfur cluster biosynthesis. J Mol Biol, 383, 133-143. PubMed id: 18723024 DOI: 10.1016/j.jmb.2008.08.015

Date:

20-Aug-07 Release date: 19-Aug-08

Protein chains

O67045  (ISCU_AQUAE) -  Iron-sulfur cluster assembly scaffold protein IscU from Aquifex aeolicus (strain VF5)

Seq: 157 a.a.

Struc: 139 a.a.*

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

DOI no: 10.1016/j.jmb.2008.08.015

J Mol Biol 383:133-143 (2008)

PubMed id: 18723024

The asymmetric trimeric architecture of [2Fe-2S] IscU: implications for its scaffolding during iron-sulfur cluster biosynthesis.

Y.Shimomura, K.Wada, K.Fukuyama, Y.Takahashi.

ABSTRACT

IscU is a key component of the ISC machinery and is involved in the biogenesis of iron-sulfur (Fe-S) proteins. IscU serves as a scaffold for assembly of a nascent Fe-S cluster prior to its delivery to an apo protein. Here, we report the first crystal structure of IscU with a bound [2Fe-2S] cluster from the hyperthermophilic bacterium Aquifex aeolicus, determined at a resolution of 2.3 A, using multiwavelength anomalous diffraction of the cluster. The holo IscU formed a novel asymmetric trimer that harbored only one [2Fe-2S] cluster. One iron atom of the cluster was coordinated by the S(gamma) atom of Cys36 and the N(epsilon) atom of His106, and the other was coordinated by the S(gamma) atoms of Cys63 and Cys107 on the surface of just one of the protomers. However, the cluster was buried inside the trimer between the neighboring protomers. The three protomers were conformationally distinct from one another and associated around a noncrystallographic pseudo-3-fold axis. The three flexible loop regions carrying the ligand-binding residues (Cys36, Cys63, His106 and Cys107) and the N-terminal alpha1 helices were positioned at the interfaces and underwent substantial conformational rearrangement, which stabilized the association of the asymmetric trimer. This unique trimeric A. aeolicus holo-IscU architecture was clearly distinct from other known monomeric apo-IscU/SufU structures, indicating that asymmetric trimer organization, as well as its association/dissociation, would be involved in the scaffolding function of IscU.

Selected figure(s)

Figure 1.
Fig. 1. The crystal structure of Aa holo IscU. (a) Overall structure of the asymmetric trimer. The conformationally distinct protomers A, B and C are shown in pink, green and blue, respectively. The [2Fe–2S] cluster is shown as a red rhombus. (b) Structure of protomer B and its [2Fe–2S] cluster. The α helices (green, α1–α6), β strands (orange, β1–β3), loop regions (magenta, L1–L8) and iron (cyan) and sulfur (yellow) atoms are depicted.

Figure 5.
Fig. 5. Structural comparison among the IscU/SufU homologs. Ribbon diagrams are shown for (upper row) Aa IscU protomers A, B and C and (bottom row) Hi IscU [Protein Data Bank (PDB) ID 1R9P], Mm IscU (PDB ID 1WFZ), Sp SufU (PDB ID 1SU0) and Bs SufU (PDB ID 2AZH). The Aa IscU α3 (Ile82–Leu86) and α4 (Tyr90–Glu96) helices (and their corresponding regions) are shown in green, and the L7 loops are shown in magenta. The SufU-specific insertions are denoted in cyan: Gln101–Ala119 in Sp SufU and Lys102–Ser120 in Bs SufU. The N-terminal region of Hi IscU was disordered in the NMR structure and omitted from the model. In the Mm IscU structure, the N-terminal amino acids were truncated and replaced with unrelated sequence during the plasmid construction.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 133-143) copyright 2008.

Figures were selected by an automated process.