PDBsum entry 2e6c

Hydrolase

PDB id: 2e6c

Contents

Protein chains

243 a.a. *

Ligands

SO4 ×9

GOL ×2

Metals

_MN ×4

Waters ×304

* Residue conservation analysis

PDB id:

2e6c

Name:

Hydrolase

Title:

Crystal structure of the stationary phase survival protein sure from thermus thermophilus hb8 cocrystallized with manganese and amp

Structure:

5'-nucleotidase sure. Chain: a, b, c, d. Synonym: stationary phase survival protein sure, nucleoside 5'- monophosphate phosphohydrolase. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.05Å R-factor: 0.208 R-free: 0.249

Authors:

W.Iwasaki,K.Miki

Key ref:

W.Iwasaki and K.Miki (2007). Crystal structure of the stationary phase survival protein SurE with metal ion and AMP. J Mol Biol, 371, 123-136. PubMed id: 17561111 DOI: 10.1016/j.jmb.2007.05.007

Date:

26-Dec-06 Release date: 28-Aug-07

Protein chains

Q53W92  (SURE_THET8) -  5'-nucleotidase SurE from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 244 a.a.

Struc: 243 a.a.

Enzyme reactions

• Enzyme class: 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 = GOL) matches with 60.00% similarity) + phosphate

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

Added reference

DOI no: 10.1016/j.jmb.2007.05.007

J Mol Biol 371:123-136 (2007)

PubMed id: 17561111

Crystal structure of the stationary phase survival protein SurE with metal ion and AMP.

W.Iwasaki, K.Miki.

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. 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.

Selected figure(s)

Figure 2.
Figure 2. Tetrameric structures of SurE proteins. (a) Structure of TtSurE-MnAMP. Each protomer is given a different color and labeled A to D. Three non-crystallographic pseudo 2-fold axes are labeled p, q, and r. AMP and Mn^2+ are depicted as magenta stick models and spheres, respectively. The C[α] atoms of invariant Asp8 are connected with dotted lines to compare the arrangements of the protomers. The right-hand panel shows the side view rotated by 90° around the p axis. (b) Tetrameric structure of TmSurE complexed with Ca^2+ and tungstate (PDB code 1J9K).^6 Tungstate groups are shown as magenta stick models, and calcium ions are shown as spheres. (c) Structure of the tetramer of PaSurE (PDB code 1L5X).^8 The Figure was prepared with MOLSCRIPT,^19 and rendered with Raster3D.^20

Figure 5.
Figure 5. Arrangement of the active sites and the C[α] traces of the loops 34-50 in the tetramer of TtSurE-MnAMP. The bound manganese ions and AMP models are shown in magenta.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 123-136) copyright 2007.

Figures were selected by an automated process.