Database accession: MF7000225
Name: SurE, E112A mutant F222 form (Salmonella typhimurium)
PDB ID: 4ryt
Experimental method: X-ray (2.09 Å)
Assembly: Homodimer
Source organism: Salmonella typhimurium
Primary publication of the structure:
Mathiharan YK, Savithri HS, Murthy MR
Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.
(2015) Acta Crystallogr. D Biol. Crystallogr. 71: 1812-23
PMID: 26327371
Abstract:
The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of β-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167°. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11° between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.
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, A-2
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: 1-253)
Coverage: 100%
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: 1-253)
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: 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 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)
Download this entry's XML file (.xml)
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