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: 63.15 kDa 
• Atom Count: 4817 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 1

1TD2

Crystal Structure of the PdxY Protein from Escherichia coli

• PDB DOI: 10.2210/pdb1TD2/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-21 Released: 2004-07-13 
• Deposition Author(s): Safo, M.K., Musayev, F.N., Hunt, S., di Salvo, M., Scarsdale, N., Schirch, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Crystal structure of the PdxY Protein from Escherichia coli

Safo, M.K., Musayev, F.N., Hunt, S., di Salvo, M.L., Scarsdale, N., Schirch, V.

(2004) J Bacteriol 186: 8074-8082

• PubMed: 15547280 
• DOI: 10.1128/JB.186.23.8074-8082.2004
• Primary Citation of Related Structures:  
  1TD2


• PubMed Abstract: 
  

The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA . [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine kinase	A, B	287	Escherichia coli	Mutation(s): 0  Gene Names: pdxY, b1636 EC: 2.7.1.35
UniProt
Find proteins for P77150 (Escherichia coli (strain K12)) Explore P77150  Go to UniProtKB:  P77150

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXL	C [auth A], E [auth B]	3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE C8 H9 N O3 RADKZDMFGJYCBB-UHFFFAOYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.13	α = 90
b = 67.375	β = 93.67
c = 73.589	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-21 
• Released Date: 2004-07-13 
Deposition Author(s): Safo, M.K., Musayev, F.N., Hunt, S., di Salvo, M., Scarsdale, N., Schirch, V.

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance