Database accession: MF7000744
Name: Type 3 CDGSH iron-sulfur protein
PDB ID: 3tbo
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Pyrobaculum calidifontis
Primary publication of the structure:
Lin J, Zhang L, Lai S, Ye K
Structure and molecular evolution of CDGSH iron-sulfur domains.
(2011) PLoS ONE 6: e24790
PMID: 21949752
Abstract:
The recently discovered CDGSH iron-sulfur domains (CISDs) are classified into seven major types with a wide distribution throughout the three domains of life. The type 1 protein mitoNEET has been shown to fold into a dimer with the signature CDGSH motif binding to a [2Fe-2S] cluster. However, the structures of all other types of CISDs were unknown. Here we report the crystal structures of type 3, 4, and 6 CISDs determined at 1.5 Å, 1.8 Å and 1.15 Å resolution, respectively. The type 3 and 4 CISD each contain one CDGSH motif and adopt a dimeric structure. Although similar to each other, the two structures have permutated topologies, and both are distinct from the type 1 structure. The type 6 CISD contains tandem CDGSH motifs and adopts a monomeric structure with an internal pseudo dyad symmetry. All currently known CISD structures share dual iron-sulfur binding modules and a β-sandwich for either intermolecular or intramolecular dimerization. The iron-sulfur binding module, the β-strand N-terminal to the module and a proline motif are conserved among different type structures, but the dimerization module and the interface and orientation between the two iron-sulfur binding modules are divergent. Sequence analysis further shows resemblance between CISD types 4 and 7 and between 1 and 2. Our findings suggest that all CISDs share common ancestry and diverged into three primary folds with a characteristic phylogenetic distribution: a eukaryote-specific fold adopted by types 1 and 2 proteins, a prokaryote-specific fold adopted by types 3, 4 and 7 proteins, and a tandem-motif fold adopted by types 5 and 6 proteins. Our comprehensive structural, sequential and phylogenetic analysis provides significant insight into the assembly principles and evolutionary relationship of CISDs.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
2 iron, 2 sulfur cluster binding 2 iron, 2 sulfur cluster binding
metal ion binding metal ion binding
Biological process: not assigned
Cellular component:
cytoplasm cytoplasm
intracellular membrane-bounded organelle intracellular membrane-bounded organelle
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Zinc finger, CDGSH-type domain protein
Source organism: Pyrobaculum calidifontis
Length: 53 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAVEIRAIENGPYEVKIGGRAIYLCRCGHSGSKPHCDGTHAKVGFKAPGAKIV
UniProtKB AC: A3MW14 (positions: 3-53)
Coverage: 96%
Name: Zinc finger, CDGSH-type domain protein
Source organism: Pyrobaculum calidifontis
Length: 53 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAVEIRAIENGPYEVKIGGRAIYLCRCGHSGSKPHCDGTHAKVGFKAPGAKIV
UniProtKB AC: A3MW14 (positions: 3-53)
Coverage: 96%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Iron-binding zinc finger CDGSH type
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Size exclusion chromatography measurements suggest that mitoNEET33–108 protein exists as a dimer in solution (PMID:17905743). The monomers associate along their full length to form an intertwined structure with an extensive interface (PMID:17766439).
Chain A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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