8H7Y

Trans-3/4-proline-hydroxylase H11 with AKG and L-proline

• PDB DOI: https://doi.org/10.2210/pdb8H7Y/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): uncultured bacterium esnapd13
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-21 Released: 2023-04-19 
• Deposition Author(s): Gong, W.M., Hu, X.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.216 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation.

Hu, X., Huang, X., Liu, J., Zheng, P., Gong, W., Yang, L.

(2023) Acta Crystallogr D Struct Biol 79: 318-325

• PubMed: 36974966 
• DOI: https://doi.org/10.1107/S2059798323001936
• Primary Citation of Related Structures:  
  8H7T, 8H7V, 8H7Y, 8H81, 8H85


• PubMed Abstract: 
  

  L-Proline hydroxylase is a member of the non-heme Fe ²⁺ /α-ketoglutarate (AKG)-dependent hydroxylase family that catalyzes the reaction from L-proline to hydroxy-L-proline, which is widely used in drug synthesis, biochemistry, food supplementation and cosmetic industries. Here, the first crystal structure of L-proline trans-hydroxylase and its complexes with substrate and product are reported, which reveal the structural basis of trans-cis proline hydroxylation selectivity. Structure comparison with other AKG-dependent hydroxylases identifies conserved amino acid residues, which may serve as signatures of in-line or off-line AKG binding modes in the AKG-dependent enzyme family.

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Organizational Affiliation: 

Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.85 kDa 
• Atom Count: 4,555 
• Modelled Residue Count: 534 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytanoyl-CoA dioxygenase	A, B	268	uncultured bacterium esnapd13	Mutation(s): 0
UniProt
Find proteins for S5TUM1 (uncultured bacterium esnapd13) Explore S5TUM1  Go to UniProtKB:  S5TUM1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	D [auth A], G [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
PRO (Subject of Investigation/LOI)	E [auth A], H [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
FE (Subject of Investigation/LOI)	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.216 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.437	α = 90
b = 106.437	β = 90
c = 145.016	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Gong, W.M., Hu, X.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection