1A54

PHOSPHATE-BINDING PROTEIN MUTANT A197C LABELLED WITH A COUMARIN FLUOROPHORE AND BOUND TO DIHYDROGENPHOSPHATE ION

• PDB DOI: https://doi.org/10.2210/pdb1A54/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-02-19 Released: 1998-10-14 
• Deposition Author(s): Hirshberg, M., Henrick, K., Lloyd-Haire, L., Vasisht, N., Brune, M., Corrie, J.E.T., Webb, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 

Literature

Crystal structure of phosphate binding protein labeled with a coumarin fluorophore, a probe for inorganic phosphate.

Hirshberg, M., Henrick, K., Haire, L.L., Vasisht, N., Brune, M., Corrie, J.E., Webb, M.R.

(1998) Biochemistry 37: 10381-10385

• PubMed: 9671506 
• DOI: https://doi.org/10.1021/bi980428z
• Primary Citation of Related Structures:  
  1A54, 1A55


• PubMed Abstract: 
  

  Crystal structures are presented for the A197C mutant of Escherichia coli phosphate binding protein (PBP) and the same mutant labeled at Cys197 with N-[2-(1-maleimidyl)ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC). Both proteins are complexed with inorganic phosphate. The latter molecule, MDCC-PBP, exhibits a large increase in fluorescence on binding inorganic phosphate. The resulting high-fluorescence state of the coumarin and the ability of this coumarin to monitor the conformational changes associated with inorganic phosphate binding are interpreted in terms of the specific interactions of MDCC with the protein. The structure helps to explain why this particular label gives a high-fluorescence state on binding inorganic phosphate, while several other related labels do not, and hence aids our general understanding of environmentally sensitive fluorescence probes on proteins.

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Organizational Affiliation: 

Division of Protein Structure, National Institute for Medical Research, Mill Hill, London, U.K. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.97 kDa 
• Atom Count: 2,817 
• Modelled Residue Count: 321 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate-binding protein PstS	A	321	Escherichia coli	Mutation(s): 1  Gene Names: pstS, BvCmsKKP036_01783, EYX47_15990
UniProt
Find proteins for P0AG82 (Escherichia coli (strain K12)) Explore P0AG82  Go to UniProtKB:  P0AG82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MDC	C [auth A]	N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE C20 H21 N3 O5 OJBZDUMTXGGVSP-KTKRTIGZSA-N
2HP	B [auth A]	DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.498	α = 90
b = 62.651	β = 90
c = 122.608	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Hirshberg, M., Henrick, K., Lloyd-Haire, L., Vasisht, N., Brune, M., Corrie, J.E.T., Webb, M.R.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Advisory, Database references, Derived calculations, Other
• Version 2.0: 2022-08-10
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-08-02
  Changes: Refinement description