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 

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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:  
    5XF9, 5XFA

  • 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 arrangements of the subunits and Fe-S clusters are unclear ...

    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 hydrogenaseA, E591Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxF, HPTL_1420
UniProt
Find proteins for A0A077L6X8 (Hydrogenophilus thermoluteolus)
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Entity Groups  
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UniProt GroupA0A077L6X8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenaseB, F242Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxU, HPTL_1421
UniProt
Find proteins for A0A077L885 (Hydrogenophilus thermoluteolus)
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UniProt GroupA0A077L885
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenaseC, G189Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxY, HPTL_1422
UniProt
Find proteins for A0A077L7R5 (Hydrogenophilus thermoluteolus)
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UniProt GroupA0A077L7R5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-reducing hydrogenaseD, H468Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: hoxH, HPTL_1423
UniProt
Find proteins for A0A077LAI5 (Hydrogenophilus thermoluteolus)
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UniProt GroupA0A077LAI5
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
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I [auth A],
R [auth E]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
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J [auth A],
K [auth B],
L [auth B],
N [auth C],
S [auth E],
J [auth A],
K [auth B],
L [auth B],
N [auth C],
S [auth E],
T [auth F],
U [auth F],
W [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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M [auth B],
V [auth F]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
FCO
Query on FCO
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O [auth D],
X [auth H]		CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N		 Ligand Interaction
3NI
Query on 3NI
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P [auth D],
Y [auth H]		NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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Q [auth D],
Z [auth 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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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JST CRESTJapanJPMJCR12M4

Revision History  (Full details and data files)

  • 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