8H7Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.216 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AKGClick on this verticalbar to view detailsBest fitted PROClick on this verticalbar to view details

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 dioxygenase
A, B
268uncultured 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
PRO (Subject of Investigation/LOI)
Query on PRO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
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 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.437α = 90
b = 106.437β = 90
c = 145.016γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AKGClick on this verticalbar to view detailsBest fitted PROClick on this verticalbar to view details

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: 2024-05-29
    Changes: Data collection