6J1F

Crystal structure of HypX from Aquifex aeolicus in complex with Tetrahydrofolic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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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: https://doi.org/10.1038/s42003-019-0631-z
  • Primary Citation of Related Structures:  
    6J0P, 6J1E, 6J1F, 6J1G, 6J1H, 6J1I, 6J1J

  • PubMed Abstract: 
  • 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 ...

    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

    3Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase regulation HoxX582Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: hoxXaq_1156
UniProt
Find proteins for O67224 (Aquifex aeolicus (strain VF5))
Explore O67224 
Go to UniProtKB:  O67224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67224
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase regulation HoxX576Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: hoxXaq_1156
UniProt
Find proteins for O67224 (Aquifex aeolicus (strain VF5))
Explore O67224 
Go to UniProtKB:  O67224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67224
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
THG
Query on THG

Download Ideal Coordinates CCD File 
D [auth A](6S)-5,6,7,8-TETRAHYDROFOLATE
C19 H23 N7 O6
MSTNYGQPCMXVAQ-RYUDHWBXSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.02α = 90
b = 123.735β = 90
c = 290.004γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17H03093

Revision History  (Full details and data files)

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