5XF9

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the redox switches in the NAD(+)-reducing soluble [NiFe]-hydrogenase

Shomura, Y.Taketa, M.Nakashima, H.Tai, H.Nakagawa, H.Ikeda, Y.Ishii, M.Igarashi, Y.Nishihara, H.Yoon, K.S.Ogo, S.Hirota, S.Higuchi, Y.

(2017) Science 357: 928-932

  • DOI: 10.1126/science.aan4497
  • Primary Citation of Related Structures:  
    5XFA, 5XF9

  • PubMed Abstract: 
  • NAD + (oxidized form of NAD:nicotinamide adenine dinucleotide)-reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD + ):quinone oxidoreductase (complex I), but the geometrical arrangemen ...

    NAD + (oxidized form of NAD:nicotinamide adenine dinucleotide)-reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD + ):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe-S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O 2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe-S clusters and may suppress production of reactive oxygen species.


    Organizational Affiliation

    SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenase AE591Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxFHPTL_1420
Find proteins for A0A077L6X8 (Hydrogenophilus thermoluteolus)
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Go to UniProtKB:  A0A077L6X8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenase BF242Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxUHPTL_1421
Find proteins for A0A077L885 (Hydrogenophilus thermoluteolus)
Explore A0A077L885 
Go to UniProtKB:  A0A077L885
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenase CG189Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxYHPTL_1422
Find proteins for A0A077L7R5 (Hydrogenophilus thermoluteolus)
Explore A0A077L7R5 
Go to UniProtKB:  A0A077L7R5
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenase DH468Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxHHPTL_1423
Find proteins for A0A077LAI5 (Hydrogenophilus thermoluteolus)
Explore A0A077LAI5 
Go to UniProtKB:  A0A077LAI5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
A, E
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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A, B, C, E, F, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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B, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
D, H
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
3NI
Query on 3NI

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D, H
NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.59α = 90
b = 190.09β = 109.44
c = 124.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST CRESTJapanJPMJCR12M4

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Structure summary