8H81

Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytanoyl-CoA dioxygenase266uncultured bacterium esnapd13Mutation(s): 0 
UniProt
Find proteins for S5TUM1 (uncultured bacterium esnapd13)
Explore S5TUM1 
Go to UniProtKB:  S5TUM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5TUM1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HYP (Subject of Investigation/LOI)
Query on HYP

Download Ideal Coordinates CCD File 
B [auth A]4-HYDROXYPROLINE
C5 H9 N O3
PMMYEEVYMWASQN-DMTCNVIQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.289α = 90
b = 75.289β = 90
c = 144.544γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description