2E6H

Crystal structure of E37A mutant of the stationary phase survival protein SurE from Thermus thermophilus HB8 cocrystallized with manganese and AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP

Iwasaki, W.Miki, K.

(2007) J Mol Biol 371: 123-136

  • DOI: 10.1016/j.jmb.2007.05.007
  • Primary Citation of Related Structures:  
    2E69, 2E6B, 2E6C, 2E6E, 2E6G, 2E6H

  • PubMed Abstract: 
  • The stationary phase survival protein SurE is a metal ion-dependent phosphatase distributed among eubacteria, archaea, and eukaryotes. In Escherichia coli, SurE has activities as nucleotidase and exopolyphosphatase, and is thought to be involved in stress response ...

    The stationary phase survival protein SurE is a metal ion-dependent phosphatase distributed among eubacteria, archaea, and eukaryotes. In Escherichia coli, SurE has activities as nucleotidase and exopolyphosphatase, and is thought to be involved in stress response. However, its physiological role and reaction mechanism are unclear. We report here the crystal structures of the tetramer of SurE from Thermus thermophilus HB8 (TtSurE) both alone and crystallized with Mn(2+) and substrate AMP. In the presence of Mn(2+) and AMP, differences between the protomers were observed in the active site and in the loop located near the active site; AMP-bound active sites with the loops in a novel open conformation were found in the two protomers, and AMP-free active sites with the loops in a conventional closed conformation were found in the other two protomers. The two loops in the open conformation are entwined with each other, and this entwining is suggested to be required for enzymatic activity by site-directed mutagenesis. TtSurE exists as an equilibrium mixture of dimer and tetramer in solution. The loop-entwined structure indicates that SurE acts as a tetramer. The structural features and the absence of negative cooperativity imply the half-of-the-sites reactivity mechanism resulting from a pre-existing tendency toward structural asymmetry.


    Organizational Affiliation

    RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-nucleotidase surEA, B, C, D244Thermus thermophilus HB8Mutation(s): 1 
Gene Names: surETTHB070
EC: 3.1.3.5
UniProt
Find proteins for Q53W92 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53W92 
Go to UniProtKB:  Q53W92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53W92
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
R [auth C],
U [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.657α = 90
b = 131.657β = 90
c = 130.836γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations