Database accession: MF7001017
Name: Thermostable protein (Hyperthermophilic Virus SSV-RH)
PDB ID: 4aai
Experimental method: NMR
Assembly: Homodimer
Source organism: Sulfolobus virus Ragged Hills
Primary publication of the structure:
Schlenker C, Goel A, Tripet BP, Menon S, Willi T, Dlakić M, Young MJ, Lawrence CM, Copié V
Structural studies of E73 from a hyperthermophilic archaeal virus identify the "RH3" domain, an elaborated ribbon-helix-helix motif involved in DNA recognition.
(2012) Biochemistry 51: 2899-910
PMID: 22409376
Abstract:
Hyperthermophilic archaeal viruses, including Sulfolobus spindle-shaped viruses (SSVs) such as SSV-1 and SSV-Ragged Hills, exhibit remarkable morphology and genetic diversity. However, they remain poorly understood, in part because their genomes exhibit limited or unrecognizable sequence similarity to genes with known function. Here we report structural and functional studies of E73, a 73-residue homodimeric protein encoded within the SSV-Ragged Hills genome. Despite lacking significant sequence similarity, the nuclear magnetic resonance (NMR) structure reveals clear similarity to ribbon-helix-helix (RHH) domains present in numerous proteins involved in transcriptional regulation. In vitro double-stranded DNA (dsDNA) binding experiments confirm the ability of E73 to bind dsDNA in a nonspecific manner with micromolar affinity, and characterization of the K11E variant confirms the location of the predicted DNA binding surface. E73 is distinct, however, from known RHH domains. The RHH motif is elaborated upon by the insertion of a third helix that is tightly integrated into the structural domain, giving rise to the "RH3" fold. Within the homodimer, this helix results in the formation of a conserved, symmetric cleft distal to the DNA binding surface, where it may mediate protein-protein interactions or contribute to the high thermal stability of E73. Analysis of backbone amide dynamics by NMR provides evidence of a rigid core, fast picosecond to nanosecond time scale NH bond vector motions for residues located within the antiparallel β-sheet region of the proposed DNA-binding surface, and slower microsecond to millisecond time scale motions for residues in the α1-α2 loop. The roles of E73 and its SSV homologues in the viral life cycle are discussed.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: ORF E73
Source organism: Sulfolobus virus Ragged Hills
Length: 73 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK
UniProtKB AC: Q6TRU9 (positions: 1-73)
Coverage: 100%
Name: ORF E73
Source organism: Sulfolobus virus Ragged Hills
Length: 73 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK
UniProtKB AC: Q6TRU9 (positions: 1-73)
Coverage: 100%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Similarity to ribbon-helix-helix (RHH) domains is present in numerous proteins involved in transcriptional regulation. The RHH motif is elaborated upon by the insertion of a third helix that is tightly integrated into the structural domain. Thermal stability data were analyzed assuming a two-state transition of a folded dimer to two unfolded monomers without intermediates. SEC, AUC, DLS and NMR spectroscopy all indicated that E73 is a homodimer in solution (PMID:22409376).
Chain A:
N/A
Chain B:
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). No related structure was found in the MFIB database.
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