5HXI

2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti

Kobayashi, J.Yoshida, H.Yagi, T.Kamitori, S.Hayashi, H.Mizutani, K.Takahashi, N.Mikami, B.

(2017) J Biosci Bioeng 123: 154-162

  • DOI: https://doi.org/10.1016/j.jbiosc.2016.07.022
  • Primary Citation of Related Structures:  
    5HXI

  • PubMed Abstract: 

    The flavoenzyme 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) catalyzes the cleavage of the pyridine ring of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) in the presence of NADH, molecular oxygen, and water. MHPCO also catalyzes the NADH oxidation reaction uncoupled with ring opening in the absence of MHPC (the basal activity). The enzyme shows activity toward not only MHPC but also 5-hydroxynicotinic acid (5HN) and 5-pyridoxic acid (5PA). The reaction rate toward 5PA is extremely low (5% of the activity toward MHPC or 5HN). We determined the crystal structures of MHPCO without substrate and the MHPCO/5HN and MHPCO/5PA complexes, together with a Y270F mutant without substrate and its 5HN complex. The Tyr270 residue was located in the active site and formed hydrogen bonds between the Oη and water molecules to make the active site hydrophilic. Although Tyr270 took a fixed conformation in the structures of the MHPCO and MHPCO/5HN complex, it took two conformations in its 5PA complex, accompanied by two conformations of the bound 5PA. In the wild-type (WT) enzyme, the turnover number of the ring-opening activity was 6800 times that of the basal activity (1300 and 0.19 s -1 , respectively), whereas no such difference was observed in the Y270F (19 and 7.4 s -1 ) or Y270A (0.05 and 0.84 s -1 ) mutants. In the Y270F/5HN complex, the substrate bound ∼1 Å farther away than in the WT enzyme. These results revealed that Tyr270 is essential to maintain the WT conformation, which in turn enhances the coupling of the NADH oxidation with the ring-opening reaction.


  • Organizational Affiliation

    Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan. Electronic address: jk_virtue_0216@yahoo.co.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase379Mesorhizobium japonicum MAFF 303099Mutation(s): 0 
Gene Names: mlr6788
UniProt
Find proteins for Q988D3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Explore Q988D3 
Go to UniProtKB:  Q988D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ988D3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
5HN
Query on 5HN

Download Ideal Coordinates CCD File 
D [auth A]5-hydroxypyridine-3-carboxylic acid
C6 H5 N O3
ATTDCVLRGFEHEO-UHFFFAOYSA-N
PEG
Query on PEG

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K [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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G [auth A],
H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

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C [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
NA
Query on NA

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E [auth A],
F [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.338α = 90
b = 131.14β = 90
c = 132.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection
  • Version 1.3: 2024-03-20
    Changes: Advisory, Data collection, Database references