5YSW

Crystal Structure Analysis of Rif16 in complex with R-L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

  • DOI: 10.1038/s41467-018-04772-x
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    University of Chinese Academy of Sciences, 100049, Beijing, China. lishengying@qibebt.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450A441Amycolatopsis mediterranei U32Mutation(s): 0 
Gene Names: AMED_0653
UniProt
Find proteins for A0A0H3CVZ6 (Amycolatopsis mediterranei (strain U-32))
Explore A0A0H3CVZ6 
Go to UniProtKB:  A0A0H3CVZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3CVZ6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9LF
Query on 9LF

Download Ideal Coordinates CCD File 
C [auth A](2S,12E,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-5,6,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-9-yl hydroxyacetate
C39 H49 N O14
OCUBKDJIPNISSD-WPPPCPPGSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.082α = 90
b = 70.709β = 94
c = 80.975γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release