6JVW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

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This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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. Electronic address: kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
maleylpyruvate hydrolaseA, B304Sphingobium sp. SYK-6Mutation(s): 0 
Gene Names: SLG_11280
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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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