Crystal structure of maleylpyruvate hydrolase from Sphingobium sp. SYK-6 in complex with manganese (II) ion and pyruvate

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls.

Hong, H.Seo, H.Kim, K.J.

(2019) Biochem Biophys Res Commun 514: 765-771

  • DOI: https://doi.org/10.1016/j.bbrc.2019.05.030
  • Primary Citation of Related Structures:  
    6JVV, 6JVW

  • PubMed Abstract: 

    Sphingobium sp. strain SYK-6, an aerobic gram-negative bacillus found in soil, is known for utilizing lignin-derived monoaryls and biaryls as carbon sources and degrading aromatic compounds. The Sphingobium sp. strain SYK-6 genome contains three genes involved in salicylate catabolism: SLG_11260, SLG_11270, and SLG_11280. Here, we report that the gene product of SLG_11280 functions as a maleylpyruvate hydrolase (SsMPH) with K m and K cat values of 166.2 μM and 3.76 min -1 , respectively. This study also reveals the crystal structures of both the apo and pyruvate-manganese ion-bound SsMPH, which revealed that like other fumarylacetoacetate hydrolases, SsMPH dimerizes and has nine unique 3 10 -helices. Molecular docking studies of maleylpyruvate also revealed the likely binding mode of SsMPH and its substrate.

  • Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
maleylpyruvate hydrolase
A, B
304Sphingobium sp. SYK-6Mutation(s): 0 
Gene Names: SLG_11280
Find proteins for G2IPX5 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Explore G2IPX5 
Go to UniProtKB:  G2IPX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2IPX5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.409α = 90
b = 74.181β = 119.07
c = 68.727γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-22
    Changes: Refinement description