4QVG | pdb_00004qvg

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

• PDB DOI: https://doi.org/10.2210/pdb4QVG/pdb

• Classification: TRANSFERASE
• Organism(s): Streptosporangium sibiricum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-15 Released: 2015-05-27 
• Deposition Author(s): Liu, J.S., Chen, S.C., Huang, C.H., Yang, C.S., Chen, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.266 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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

• PubMed: 25960001 
• DOI: https://doi.org/10.1038/srep10100
• Primary Citation 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. 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.
Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
1] Division of Critical Care &Respiratory Therapy, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan [2] Department of Applied Chemistry, National Chi Nan University, Nantou County, Taiwan.
1] Department of Food and Nutrition, Providence University, Taichung, Taiwan [2] Department of Endocrinology and Metabolism, Kuang Tien General Hospital, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Department of Biotechnology, Hungkuang University, Taichung, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.7 kDa 
• Atom Count: 10,596 
• Modeled Residue Count: 1,370 
• Deposited Residue Count: 1,420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SibL	A, B, C, D	355	Streptosporangium sibiricum	Mutation(s): 0  Gene Names: sibL
UniProt
Find proteins for C0LTM6 (Streptosporangium sibiricum) Explore C0LTM6  Go to UniProtKB:  C0LTM6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.266 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.931	α = 90
b = 295.421	β = 90
c = 322.231	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Liu, J.S., Chen, S.C., Huang, C.H., Yang, C.S., Chen, Y.

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description