5KIK

CmlA beta-hydroxylase in chemically reduced diferrous state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme beta-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase.

Jasniewski, A.J.Knoot, C.J.Lipscomb, J.D.Que, L.

(2016) Biochemistry 55: 5818-5831

  • DOI: 10.1021/acs.biochem.6b00834
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinucle ...

    The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinuclear iron cluster that is reduced to the diferrous state (WT R ) to initiate O 2 activation. However, rapid O 2 activation occurs only when WT R is bound to CmlP, the NRPS to which l-PAPA is covalently attached. Here the X-ray crystal structure of WT R is reported, which is very similar to that of the as-isolated diferric enzyme in which the irons are coordinately saturated. X-ray absorption spectroscopy is used to investigate the WT R cluster ligand structure as well as the structures of WT R in complex with a functional CmlP variant (CmlP AT ) with and without l-PAPA attached. It is found that formation of the active WT R :CmlP AT -l-PAPA complex converts at least one iron of the cluster from six- to five-coordinate by changing a bidentately bound amino acid carboxylate to monodentate on Fe1. The only bidentate carboxylate in the structure of WT R is E377. The crystal structure of the CmlA variant E377D shows only monodentate carboxylate coordination. Reduced E377D reacts rapidly with O 2 in the presence or absence of CmlP AT -l-PAPA, showing loss of regulation. However, this variant fails to catalyze hydroxylation, suggesting that E377 has the dual role of coupling regulation of O 2 reactivity with juxtaposition of the substrate and the reactive oxygen species. The carboxylate shift in response to substrate binding represents a novel regulatory strategy for oxygen activation in diiron oxygenases.


    Organizational Affiliation

    Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455.,Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CmlA protein
A
551Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)Mutation(s): 0 
Gene Names: cmlA
EC: 1.14.99.65
Find proteins for F2RB80 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Go to UniProtKB:  F2RB80
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 153.529α = 90.00
b = 153.529β = 90.00
c = 93.043γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM100943
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118030

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence