3GMB | pdb_00003gmb

Crystal Structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid Oxygenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.224 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

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This is version 1.4 of the entry. See complete history. 

Literature

Structure of the PLP degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications.

McCulloch, K.M., Mukherjee, T., Begley, T.P., Ealick, S.E.

(2009) Biochemistry 48: 4139-4149

  • DOI: https://doi.org/10.1021/bi900149f
  • Primary Citation Related Structures: 
    3GMB, 3GMC

  • PubMed Abstract: 

    A vitamin B(6) degradative pathway has recently been identified and characterized in Mesorhizobium loti MAFF303099. One of the enzymes on this pathway, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO), is a flavin-dependent enzyme and catalyzes the oxidative ring-opening of 2-methyl-3-hydroxypyridine-5-carboxylic acid to form E-2-(acetamino-methylene)succinate. The gene for this enzyme has been cloned, and the corresponding protein has been overexpressed in Escherichia coli and purified. The crystal structure of MHPCO has been solved to 2.1 A using SAD phasing with and without the substrate MHPC bound. These crystal structures provide insight into the reaction mechanism and suggest roles for active site residues in the catalysis of a novel oxidative ring-opening reaction.

    • Organizational Affiliation: 
    • Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Macromolecule Content 

  • Total Structure Weight: 94.08 kDa 
  • Atom Count: 6,580 
  • Modeled Residue Count: 738 
  • Deposited Residue Count: 830 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
A, B
415Mesorhizobium lotiMutation(s): 0 
Gene Names: mlr6788
EC: 1.14.13.242
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
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.224 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.28α = 90
b = 130.2β = 122.6
c = 89.54γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-26
    Changes: Other, Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary