4QVG

Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in its apo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase

Chen, S.C., Huang, C.H., Lai, S.J., Liu, J.S., Fu, P.K., Tseng, S.T., Yang, C.S., Lai, M.C., Ko, T.P., Chen, Y.

(2015) Sci Rep 5: 10100-10100

  • DOI: 10.1038/srep10100

  • PubMed Abstract: 

    • Streptosporangium sibiricum SibL catalyzes the methyl transfer from S-adenosylmethionine (SAM) to 3-hydroxykynurenine (3-HK) to produce S-adenosylhomocysteine (SAH) and 3-hydroxy-4-methyl-kynurenine for sibiromycin biosynthesis. Here, we present the ...

    Streptosporangium sibiricum SibL catalyzes the methyl transfer from S-adenosylmethionine (SAM) to 3-hydroxykynurenine (3-HK) to produce S-adenosylhomocysteine (SAH) and 3-hydroxy-4-methyl-kynurenine for sibiromycin biosynthesis. Here, we present the crystal structures of apo-form Ss-SibL, Ss-SibL/SAH binary complex and Ss-SibL/SAH/3-HK ternary complex. Ss-SibL is a homodimer. Each subunit comprises a helical N-terminal domain and a Rossmann-fold C-terminal domain. SAM (or SAH) binding alone results in domain movements, suggesting a two-step catalytic cycle. Analyses of the enzyme-ligand interactions and further mutant studies support a mechanism in which Tyr134 serves as the principal base in the transferase reaction of methyl group from SAM to 3-HK.

    Organizational Affiliation: 

    1] Department of Biotechnology, Hungkuang University, Taichung, Taiwan [2] Taiwan Advance Biopharm (TABP), Inc., Xizhi City, New Taipei City, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SibL
A, B, C, D
355Streptosporangium sibiricumMutation(s): 0 
Gene Names: sibL
Find proteins for C0LTM6 (Streptosporangium sibiricum)
Go to UniProtKB:  C0LTM6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.931α = 90.00
b = 295.421β = 90.00
c = 322.231γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release