3AJ3

Crystal structure of selenomethionine substituted 4-pyridoxolactonase from Mesorhizobium loti

• PDB DOI:  https://doi.org/10.2210/pdb3AJ3/pdb

• Classification: HYDROLASE
• Organism(s): Mesorhizobium loti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2011-05-25 
• Deposition Author(s): Kobayashi, J., Yoshikane, Y., Baba, S., Mikami, B., Yagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structure of 4-pyridoxolactonase from Mesorhizobium loti.

Kobayashi, J., Yoshikane, Y., Yagi, T., Baba, S., Mizutani, K., Takahashi, N., Mikami, B.

(2014) Acta Crystallogr F Struct Biol Commun 70: 424-432

• PubMed: 24699732 
• DOI: https://doi.org/10.1107/S2053230X14003926
• Primary Citation of Related Structures:  
  3AJ3, 4KEP, 4KEQ


• PubMed Abstract: 
  

4-Pyridoxolactonase from Mesorhizobium loti catalyzes the zinc-dependent lactone-ring hydrolysis of 4-pyridoxolactone (4PAL) to 4-pyridoxic acid (4PA) in vitamin B6 degradation pathway I. The crystal structures of 4-pyridoxolactonase and its complex with 5-pyridoxolactone (5PAL; the competitive inhibitor) were determined. The overall structure was an αβ/βα sandwich fold, and two zinc ions were coordinated. This strongly suggested that the enzyme belongs to subclass B3 of the class B β-lactamases. In the complex structure, the carbonyl group of 5PAL pointed away from the active site, revealing why it acts as a competitive inhibitor. Based on docking simulation with 4PAL, 4PA and a reaction intermediate, 4-pyridoxolactonase probably catalyzes the reaction through a subclass B2-like mechanism, not the subclass B3 mechanism.

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Organizational Affiliation: 

Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.

Biological Assembly 1  

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: 31.19 kDa 
• Atom Count: 2,568 
• Modelled Residue Count: 273 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-pyridoxolactonase	A	274	Mesorhizobium loti	Mutation(s): 0  Gene Names: mlr6805 EC: 3.1.1.27
UniProt
Find proteins for Q988B9 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q988B9  Go to UniProtKB:  Q988B9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.777	α = 90
b = 39.214	β = 117.92
c = 84.191	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXE	model building
RESOLVE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Kobayashi, J., Yoshikane, Y., Baba, S., Mikami, B., Yagi, T.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-04-09
  Changes: Database references
• Version 1.3: 2020-01-01
  Changes: Database references, Derived calculations