Database accession: MF7000224
Name: SurE D230A/H234A mutant (Salmonella typhimurium)
PDB ID: 4gad
Experimental method: X-ray (2.35 Å)
Assembly: Homodimer
Source organism: Salmonella typhimurium
Primary publication of the structure:
Mathiharan YK, Pappachan A, Savithri HS, Murthy MR
Dramatic structural changes resulting from the loss of a crucial hydrogen bond in the hinge region involved in C-terminal helix swapping in SurE: a survival protein from Salmonella typhimurium.
(2013) PLoS ONE 8: e55978
PMID: 23409101
Abstract:
Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two β strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 Å and 2.35 Å resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2- H234 NE2 hydrogen bond (2.89 Å in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
3'-nucleotidase activity 3'-nucleotidase activity
5'-nucleotidase activity 5'-nucleotidase activity
exopolyphosphatase activity exopolyphosphatase activity
metal ion binding metal ion binding
nucleotide binding nucleotide binding
XMP 5'-nucleosidase activity XMP 5'-nucleosidase activity
Biological process: not assigned
Cellular component:
cytoplasm cytoplasm
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: 5'/3'-nucleotidase SurE
Source organism: Salmonella typhimurium
Length: 253 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW
UniProtKB AC: P66881 (positions: 1-251)
Coverage: 99%
Name: 5'/3'-nucleotidase SurE
Source organism: Salmonella typhimurium
Length: 253 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW
UniProtKB AC: P66881 (positions: 3-253)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Survival protein SurE
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Two-state thermal unfolding (PMID:23409101). Domain-swapped dimer with extensive swap region and large dimer interface. Dimeric in solution (gel filtration, DLS).
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). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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