6J1I

Crystal structure of HypX from Aquifex aeolicus, A392F-I419F variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase.

Muraki, N.Ishii, K.Uchiyama, S.Itoh, S.G.Okumura, H.Aono, S.

(2019) Commun Biol 2: 385-385

  • DOI: 10.1038/s42003-019-0631-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several accessory proteins are required for the assembly of the metal centers in hydrogenases. In NiFe-hydrogenases, CO and CN <sup>- </sup> are coordinated to the Fe in the NiFe dinuclear cluster of the active center. Though these diatomic ligands a ...

    Several accessory proteins are required for the assembly of the metal centers in hydrogenases. In NiFe-hydrogenases, CO and CN - are coordinated to the Fe in the NiFe dinuclear cluster of the active center. Though these diatomic ligands are biosynthesized enzymatically, detail mechanisms of their biosynthesis remain unclear. Here, we report the structural characterization of HypX responsible for CO biosynthesis to assemble the active site of NiFe hydrogenase. CoA is constitutionally bound in HypX. Structural characterization of HypX suggests that the formyl-group transfer will take place from N 10 -formyl-THF to CoA to form formyl-CoA in the N-terminal domain of HypX, followed by decarbonylation of formyl-CoA to produce CO in the C-terminal domain though the direct experimental results are not available yet. The conformation of CoA accommodated in the continuous cavity connecting the N- and C-terminal domains will interconvert between the extended and the folded conformations for HypX catalysis.


    Organizational Affiliation

    1Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan.,2Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan.,3Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan.,4Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase regulation HoxX
A
582Aquifex aeolicus (strain VF5)Mutation(s): 2 
Gene Names: hoxX
Find proteins for O67224 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67224
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.701α = 90.00
b = 139.639β = 90.00
c = 167.661γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-28 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Muraki, N., Aono, S.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17H03093

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release