PDBsum entry 4xep

Hydrolase

PDB id: 4xep

Contents

Protein chain

255 a.a.

Ligands

PO4

EDO ×4

Metals

_MG

Waters ×353

PDB id:

4xep

Name:

Hydrolase

Title:

Crystal structure of f222 form of e112a/h234a mutant of stationary phase survival protein (sure) from salmonella typhimurium

Structure:

5'/3'-nucleotidase sure. Chain: a. Synonym: exopolyphosphatase,nucleoside monophosphate phosphohydrolase. Engineered: yes. Mutation: yes

Source:

Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: lt2. Gene: sure. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.189 R-free: 0.229

Authors:

Y.K.Mathiharan,M.R.N.Murthy

Key ref:

Y.K.Mathiharan et al. (2015). Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Acta Crystallogr D Biol Crystallogr, 71, 1812-1823. PubMed id: 26327371 DOI: 10.1107/S1399004715011992

Date:

24-Dec-14 Release date: 09-Sep-15

Protein chain

P66881  (SURE_SALTY) -  5'/3'-nucleotidase SurE from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 253 a.a.

Struc: 255 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.3.1.3.5 - 5'-nucleotidase.
• Reaction: a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate

ribonucleoside 5'-phosphate + H2O = ribonucleoside (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 3: E.C.3.1.3.6 - 3'-nucleotidase.
• Reaction: a ribonucleoside 3'-phosphate + H2O = a ribonucleoside + phosphate

ribonucleoside 3'-phosphate + H2O = ribonucleoside (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 4: E.C.3.6.1.11 - exopolyphosphatase.
• Reaction: [phosphate](n) + H2O = [phosphate](n-1) + phosphate + H⁺

[phosphate](n) + H2O = [phosphate](n-1) + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S1399004715011992

Acta Crystallogr D Biol Crystallogr 71:1812-1823 (2015)

PubMed id: 26327371

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.

Y.K.Mathiharan, H.S.Savithri, M.R.Murthy.

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.