Database accession: MF7000221
Name: Stationary Phase Survival Protein SurE (Salmonella typhimurium)
PDB ID: 2v4n
Experimental method: X-ray (1.70 Å)
Assembly: Homodimer
Source organism: Salmonella typhimurium
Primary publication of the structure:
Pappachan A, Savithri HS, Murthy MR
Structural and functional studies on a mesophilic stationary phase survival protein (Sur E) from Salmonella typhimurium.
(2008) FEBS J. 275: 5855-64
PMID: 19021761
Abstract:
SurE, the stationary-phase survival protein of Salmonella typhimurium, forms part of a stress survival operon regulated by the stationary-phase RNA polymerase alternative sigma factor. SurE is known to improve bacterial viability during stress conditions. It functions as a phosphatase specific to nucleoside monophosphates. In the present study we reported the X-ray crystal structure of SurE from Salmonella typhimurium. The protein crystallized in two forms: orthorhombic F222; and monoclinic C2. The two structures were determined to resolutions of 1.7 and 2.7 A, respectively. The protein exists as a domain-swapped dimer. The residue D230 is involved in several interactions that are probably crucial for domain swapping. A divalent metal ion is found at the active site of the enzyme, which is consistent with the divalent metal ion-dependent activity of the enzyme. Interactions of the conserved DD motif present at the N-terminus with the phosphate and the Mg(2+) present in the active site suggest that these residues play an important role in enzyme activity. The divalent metal ion specificity and the kinetic constants of SurE were determined using the generic phosphatase substrate para-nitrophenyl phosphate. The enzyme was inactive in the absence of divalent cations and was most active in the presence of Mg(2+). Thermal denaturation studies showed that S. typhimurium SurE is much less stable than its homologues and an attempt was made to understand the molecular basis of the lower thermal stability based on solvation free-energy. This is the first detailed crystal structure analysis of SurE from a mesophilic organism.
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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