6C3B | pdb_00006c3b

O2-, PLP-Dependent L-Arginine Hydroxylase RohP Holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.172 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6C3B

This is version 1.3 of the entry. See complete history

Literature

Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase.

Hedges, J.B.Kuatsjah, E.Du, Y.L.Eltis, L.D.Ryan, K.S.

(2018) ACS Chem Biol 13: 965-974

  • DOI: https://doi.org/10.1021/acschembio.8b00039
  • Primary Citation Related Structures: 
    6C3A, 6C3B, 6C3C, 6C3D

  • PubMed Abstract: 

    Enzymes that catalyze hydroxylation of unactivated carbons normally contain heme and nonheme iron cofactors. By contrast, how a pyridoxal phosphate (PLP)-dependent enzyme could catalyze such a hydroxylation was unknown. Here, we investigate RohP, a PLP-dependent enzyme that converts l-arginine to ( S)-4-hydroxy-2-ketoarginine. We determine that the RohP reaction consumes oxygen with stoichiometric release of H 2 O 2 . To understand this unusual chemistry, we obtain ∼1.5 Å resolution structures that capture intermediates along the catalytic cycle. Our data suggest that RohP carries out a four-electron oxidation and a stereospecific alkene hydration to give the ( S)-configured product. Together with our earlier studies on an O 2 , PLP-dependent l-arginine oxidase, our work suggests that there is a shared pathway leading to both oxidized and hydroxylated products from l-arginine.


  • Organizational Affiliation
    • Institute of Pharmaceutical Biotechnology, School of Medicine , Zhejiang University , Hangzhou , China.

Macromolecule Content 

  • Total Structure Weight: 96.34 kDa 
  • Atom Count: 6,859 
  • Modeled Residue Count: 728 
  • Deposited Residue Count: 826 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
413Streptantibioticus cattleyicolor NRRL 8057 = DSM 46488Mutation(s): 0 
Gene Names: SCATT_03970
UniProt
Find proteins for G8WNK6 (Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057))
Explore G8WNK6 
Go to UniProtKB:  G8WNK6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8WNK6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
S [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.38α = 90
b = 112.41β = 95.77
c = 102.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection