5YSM | pdb_00005ysm

Crystal Structure Analysis of Rif16

• PDB DOI: https://doi.org/10.2210/pdb5YSM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis mediterranei U32
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-14 Released: 2018-07-04 
• Deposition Author(s): Li, F.W., Qi, F.F., Xiao, Y.L., Zhao, G.P., Li, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Deciphering the late steps of rifamycin biosynthesis.

Qi, F., Lei, C., Li, F., Zhang, X., Wang, J., Zhang, W., Fan, Z., Li, W., Tang, G.L., Xiao, Y., Zhao, G., Li, S.

(2018) Nat Commun 9: 2342-2342

• PubMed: 29904078 
• DOI: https://doi.org/10.1038/s41467-018-04772-x
• Primary Citation Related Structures: 
  5YSM, 5YSW


• PubMed Abstract: 
  

  Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C-O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families.

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Organizational Affiliation: 
• Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.
CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China.
CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, 100049, Beijing, China.
Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China. [e-mail].
University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 49.4 kDa 
• Atom Count: 2,986 
• Modeled Residue Count: 364 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	441	Amycolatopsis mediterranei U32	Mutation(s): 0  Gene Names: AMED_0653
UniProt
Find proteins for A0A0H3CVZ6 (Amycolatopsis mediterranei (strain U-32)) Explore A0A0H3CVZ6  Go to UniProtKB:  A0A0H3CVZ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.234 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.105	α = 90
b = 70.335	β = 94.43
c = 81.019	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Li, F.W., Qi, F.F., Xiao, Y.L., Zhao, G.P., Li, S.Y.

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references