4P7X

L-pipecolic acid-bound L-proline cis-4-hydroxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined Regio- and Stereoselective Hydroxylation of l-Pipecolic Acid by Protein Engineering of l-Proline cis-4-Hydroxylase Based on the X-ray Crystal Structure.

Koketsu, K.Shomura, Y.Moriwaki, K.Hayashi, M.Mitsuhashi, S.Hara, R.Kino, K.Higuchi, Y.

(2015) Acs Synth Biol 4: 383-392

  • DOI: 10.1021/sb500247a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymatic regio- and stereoselective hydroxylation are valuable for the production of hydroxylated chiral ingredients. Proline hydroxylases are representative members of the nonheme Fe(2+)/α-ketoglutarate-dependent dioxygenase family. These enzymes c ...

    Enzymatic regio- and stereoselective hydroxylation are valuable for the production of hydroxylated chiral ingredients. Proline hydroxylases are representative members of the nonheme Fe(2+)/α-ketoglutarate-dependent dioxygenase family. These enzymes catalyze the conversion of L-proline into hydroxy-L-prolines (Hyps). L-Proline cis-4-hydroxylases (cis-P4Hs) from Sinorhizobium meliloti and Mesorhizobium loti catalyze the hydroxylation of L-proline, generating cis-4-hydroxy-L-proline, as well as the hydroxylation of L-pipecolic acid (L-Pip), generating two regioisomers, cis-5-Hypip and cis-3-Hypip. To selectively produce cis-5-Hypip without simultaneous production of two isomers, protein engineering of cis-P4Hs is required. We therefore carried out protein engineering of cis-P4H to facilitate the conversion of the majority of L-Pip into the cis-5-Hypip isomer. We first solved the X-ray crystal structure of cis-P4H in complex with each of L-Pro and L-Pip. Then, we conducted three rounds of directed evolution and successfully created a cis-P4H triple mutant, V97F/V95W/E114G, demonstrating the desired regioselectivity toward cis-5-Hypip.


    Organizational Affiliation

    †Bioprocess Development Center, Kyowa Hakko Bio Co., Ltd., Tsukuba, Ibaraki 305-0841, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-proline cis-4-hydroxylase
A
292Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)Mutation(s): 0 
EC: 1.14.11.56
Find proteins for Q989T9 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Go to UniProtKB:  Q989T9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AKG
Query on AKG

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Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
CXS
Query on CXS

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Download CCD File 
A
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
YCP
Query on YCP

Download SDF File 
Download CCD File 
A
(2S)-piperidine-2-carboxylic acid
C6 H11 N O2
HXEACLLIILLPRG-YFKPBYRVSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.135 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 112.680α = 90.00
b = 123.395β = 90.00
c = 56.980γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary