6C3A

O2-, PLP-dependent L-arginine hydroxylase RohP 4-hydroxy-2-ketoarginine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


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: 10.1021/acschembio.8b00039
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B413Streptomyces cattleya NRRL 8057 = DSM 46488Mutation(s): 0 
Gene Names: SCATT_03970
UniProt
Find proteins for G8WNK6 (Streptomyces cattleya (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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EGV
Query on EGV

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
(4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid
C6 H11 N3 O4
RPBOKETVUMOUHD-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
G [auth A],
H [auth A],
C [auth A],
D [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.8α = 90
b = 112.55β = 96.39
c = 101.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2016-03778
Alfred P. Sloan FoundationUnited StatesFG-20166503

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: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence