Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

 6C3B

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

• PDB DOI:  https://doi.org/10.2210/pdb6C3B/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptantibioticus cattleyicolor NRRL 8057 = DSM 46488
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-09 Released: 2018-03-07 
• Deposition Author(s): Hedges, J.B., Ryan, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.172 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

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

• PubMed: 29466666 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	413	Streptantibioticus cattleyicolor NRRL 8057 = DSM 46488	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth A], I [auth A], S [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	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
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.172 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.38	α = 90
b = 112.41	β = 95.77
c = 102.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Hedges, J.B., Ryan, K.S.

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection, Database references