Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.47 kDa 
• Atom Count: 3740 
• Modelled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

4IJ5

Crystal Structure of a Novel-type Phosphoserine Phosphatase from <i>Hydrogenobacter thermophilus</i> TK-6

• PDB DOI: 10.2210/pdb4IJ5/pdb

• Classification: HYDROLASE
• Organism(s): Hydrogenobacter thermophilus TK-6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-21 Released: 2013-03-20 
• Deposition Author(s): Chiba, Y., Horita, S., Ohtsuka, J., Arai, H., Nagata, K., Igarashi, Y., Tanokura, M., Ishii, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis

Chiba, Y., Horita, S., Ohtsuka, J., Arai, H., Nagata, K., Igarashi, Y., Tanokura, M., Ishii, M.

(2013) J Biol Chem 288: 11448-11458

• PubMed: 23479726 
• DOI: 10.1074/jbc.M112.449561
• Primary Citation of Related Structures:  
  4IJ5, 4IJ6


• PubMed Abstract: 
  

Novel-type serine-synthesizing enzymes, termed metal-independent phosphoserine phosphatases (iPSPs), were recently identified and characterized from Hydrogenobacter thermophilus, a chemolithoautotrophic bacterium belonging to the order Aquificales. iPSPs are cofactor-dependent phosphoglycerate mutase (dPGM)-like phosphatases that have significant amino acid sequence similarity to dPGMs but lack phosphoglycerate mutase activity. Genes coding dPGM-like phosphatases have been identified in a broad range of organisms; however, predicting the function of the corresponding proteins based on sequence information alone is difficult due to their diverse substrate preferences. Here, we determined the crystal structure of iPSP1 from H. thermophilus in the apo-form and in complex with its substrate L-phosphoserine to find structural units important for its phosphatase activity toward L-phosphoserine. Structural and biochemical characterization of iPSP1 revealed that the side chains of His(85) and C-terminal region characteristic of iPSP1 are responsible for the PSP activity. The importance of these structural units for PSP activity was confirmed by high PSP activity observed in two novel dPGM-like proteins from Cyanobacteria and Chloroflexus in which the two structural units were conserved. We anticipate that our present findings will facilitate understanding of the serine biosynthesis pathways of organisms that lack gene(s) encoding conventional PSPs, as the structural information revealed here will help to identify iPSP from sequence databases.

---

Organizational Affiliation: 

Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphatase 1	A, B	211	Hydrogenobacter thermophilus TK-6	Mutation(s): 0  Gene Names: pspA, pgmA, HTH_0103, Hydth_0104 EC: 3.1.3.3
UniProt
Find proteins for D3DFG8 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)) Explore D3DFG8  Go to UniProtKB:  D3DFG8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.81	α = 90
b = 73.63	β = 90
c = 124.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-21 
• Released Date: 2013-03-20 
Deposition Author(s): Chiba, Y., Horita, S., Ohtsuka, J., Arai, H., Nagata, K., Igarashi, Y., Tanokura, M., Ishii, M.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references