Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.75 kDa 
• Atom Count: 2985 
• Modelled Residue Count: 317 
• Deposited Residue Count: 322 
• Unique protein chains: 1

1D1Q

CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP

• DOI: 10.2210/pdb1D1Q/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-09-20 Released: 2000-03-08 
• Deposition Author(s): Wang, S., Tabernero, L., Zhang, M., Harms, E., Van Etten, R.L., Staufacher, C.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 

Literature

Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.

Wang, S., Tabernero, L., Zhang, M., Harms, E., Van Etten, R.L., Stauffacher, C.V.

(2000) Biochemistry 39: 1903-1914

• PubMed: 10684639 
• DOI: 10.1021/bi991348d
• Primary Citation of Related Structures:  
  1D1Q, 1D1P


• PubMed Abstract: 
  

Low-molecular weight protein tyrosine phosphatases are virtually ubiquitous, which implies that they have important cellular functions. We present here the 2.2 A resolution X-ray crystallographic structure of wild-type LTP1, a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae. We also present the structure of an inactive mutant substrate complex of LTP1 with p-nitrophenyl phosphate (pNPP) at a resolution of 1.7 A. The crystal structures of the wild-type protein and of the inactive mutant both have two molecules per asymmetric unit. The wild-type protein crystal was grown in HEPES buffer, a sulfonate anion that resembles the phosphate substrate, and a HEPES molecule was found with nearly full occupancy in the active site. Although the fold of LTP1 resembles that of its bovine counterpart BPTP, there are significant changes around the active site that explain differences in their kinetic behavior. In the crystal of the inactive mutant of LTP1, one molecule has a pNPP in the active site, while the other has a phosphate ion. The aromatic residues lining the walls of the active site cavity exhibit large relative movements between the two molecules. The phosphate groups present in the structures of the mutant protein bind more deeply in the active site (that is, closer to the position of nucleophilic cysteine side chain) than does the sulfonate group of the HEPES molecule in the wild-type structure. This further confirms the important role of the phosphate-binding loop in stabilizing the deep binding position of the phosphate group, thus helping to bring the phosphate close to the thiolate anion of nucleophilic cysteine, and facilitating the formation of the phosphoenzyme intermediate.

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Related Citations: 

• Cloning and Characterization of a Saccharomyces cerevisiae Gene Encoding the Low Molecular Weight Protein-tyrosine Phosphatase
  Ostanin, K., Pokalsky, C., Wang, S., Van Etten, R.L.
  (1995) J Biol Chem 270: 18491

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Organizational Affiliation: 

Departments of Chemistry and Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE PHOSPHATASE (E.C.3.1.3.48)	A, B	161	Saccharomyces cerevisiae	Mutation(s): 1  EC: 3.1.3.48 (PDB Primary Data), 3.1.3.2 (UniProt)
Find proteins for P40347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40347  Go to UniProtKB:  P40347

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4NP	C [auth A]	4-NITROPHENYL PHOSPHATE C6 H6 N O6 P XZKIHKMTEMTJQX-UHFFFAOYSA-N
PO4	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.897	α = 90
b = 64.151	β = 90
c = 112.049	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-20 
• Released Date: 2000-03-08 
Deposition Author(s): Wang, S., Tabernero, L., Zhang, M., Harms, E., Van Etten, R.L., Staufacher, C.V.

Revision History  

• Version 1.0: 2000-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance