4QVG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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
  • Primary Citation of Related Structures:  
    4QVG

  • 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 crystal structures of apo-form Ss-SibL, Ss-SibL/SAH binary complex and Ss-SibL/SAH/3-HK ternary complex ...

    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

    Department of Biotechnology, Hungkuang University, Taichung, Taiwan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SibLA, B, C, D355Streptosporangium sibiricumMutation(s): 0 
Gene Names: sibL
UniProt
Find proteins for C0LTM6 (Streptosporangium sibiricum)
Explore C0LTM6 
Go to UniProtKB:  C0LTM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0LTM6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.931α = 90
b = 295.421β = 90
c = 322.231γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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