1GRR | pdb_00001grr

CHLORAMPHENICOL PHOSPHOTRANSFERASE IN COMPLEX WITH 2-Nac-CHLORAMPHENICOL FROM STREPTOMYCES VENEZUELAE

• PDB DOI: https://doi.org/10.2210/pdb1GRR/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces venezuelae
• Mutation(s): No 


• Deposited: 2001-12-15 Released: 2002-01-04 
• Deposition Author(s): Izard, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.278 (Depositor) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Chloramphenicol Tolerance in Streptomyces Venezuelae by Chloramphenicol Phosphotransferase Activity

Izard, T.

(2001) Protein Sci 10: 1508

• PubMed: 11468347 
• DOI: https://doi.org/10.1002/pro.101508
• Primary Citation Related Structures: 
  1GRQ, 1GRR


• PubMed Abstract: 
  

  Streptomyces venezuelae synthesizes chloramphenicol (Cm), an inhibitor of ribosomal peptidyl transferase activity, thereby inhibiting bacterial growth. The producer escapes autoinhibition by its own secondary metabolite through phosphorylation of Cm by chloramphenicol phosphotransferase (CPT). In addition to active site binding, CPT binds its product 3-phosphoryl-Cm, in an alternate product binding site. To address the mechanisms of Cm tolerance of the producer, the crystal structures of CPT were determined in complex with either the nonchlorinated Cm (2-N-Ac-Cm) at 3.1 A resolution or the antibiotic's immediate precursor, the p-amino analog p-NH(2)-Cm, at 2.9 A resolution. Surprisingly, p-NH(2)-Cm binds CPT in a novel fashion. Additionally, neither 2-N-Ac-Cm nor p-NH(2)-Cm binds to the secondary product binding site.

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Organizational Affiliation: 
• Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 19.18 kDa 
• Atom Count: 1,424 
• Modeled Residue Count: 178 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE	A	178	Streptomyces venezuelae	Mutation(s): 0  EC: 2.7.1
UniProt
Find proteins for Q56148 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)) Explore Q56148  Go to UniProtKB:  Q56148

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLC	C [auth A]	N-ACETYL-P-NITROPHENYLSERINOL C11 H14 N2 O5 PIVQDUYOEIAFDM-GHMZBOCLSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.278 (Depositor) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200	α = 90
b = 200	β = 90
c = 200	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-04 
Deposition Author(s): Izard, T.

Revision History  

• Version 1.0: 2002-01-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description