Core domain, A-type assembly protein ATAP (ATAP_core_dom)
Type: Domain

This entry represents a common domain in ATAP proteins and related FeS cluster biogenesis proteins. It displays two α-helices and seven β-strands. In SufA from Escherichia coli, the central core consists of two β-sheets, a three-stranded sheet (short A1 and A2-A3) and a four-stranded sheet (strands B1-B4) . Several ATAP proteins displayed a similar fold (

,

). This domain is generally found as a single domain in IscA, ErpA, SufA and FeS cluster biogenesis-related proteins. In these proteins, it contains the cysteine conserved motif

, which allows them to bind FeS clusters. It could also be found at the N-terminal in NfuA and related proteins or at the C-terminal.

A-type assembly protein (ATAP) is a conserved and essential member of the ISC, SUF, and NIF systems and plays an indispensable role in the FeS cluster assembly and the transfer process. The ATAP family consists of several subfamilies:

Prokaryotic ISC system: IscA

Eukaryotic ISC system: ISCA1, ISCA2

SUF system: SufA

NIF system: HesB (IscAnif)

Additional proteins: ErpA, cpIscA

ATAPs are characterised by a conserved motif, Cys-Xn-Cys-X-Cys, by which ATAPs can bind transiently to Fe-S clusters, presumably using the three Cys residues in this motif, and transfer the FeS cluster to apoproteins .

ErpA may interact with ISC and SUF. It binds to Fe-S clusters and transfers them to apo-IspG, which is involved in quinone biosynthesis among many other cell components . It is essential for bacterial growth under aerobic conditions. cpIscA is a SufA-like ATAP that was transferred from cyanobacteria to plants through endosymbiosis events and now is only harboured by plant plastids .

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far in bacteria, three FeS assembly machineries have been identified that are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

The ISC system is conserved in eubacteria and eukaryotes (mitochondria) and has broad specificity, targeting general FeS proteins . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transferring them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .

The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoprotein targets.

In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .