5AA5

Actinobacterial-type NiFe-hydrogenase from Ralstonia eutropha H16 at 2.85 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of an Actinobacterial-Type [Nife]-Hydrogenase Reveals Insight Into O2-Tolerant H2 Oxidation.

Schafer, C.Bommer, M.Hennig, S.E.Jeoung, J.Dobbek, H.Lenz, O.

(2016) Structure 24: 285

  • DOI: 10.1016/j.str.2015.11.010
  • Primary Citation of Related Structures:  
    5AA5

  • PubMed Abstract: 
  • A novel group of bacterial [NiFe]-hydrogenases is responsible for high-affinity H2 uptake from the troposphere, and is therefore thought to play an important role in the global H2 cycle. Here we present the first crystal structure at 2.85-Å resolution of such an actinobacterial-type hydrogenase (AH), which was isolated from the dihydrogen oxidizing bacterium, Ralstonia eutropha ...

    A novel group of bacterial [NiFe]-hydrogenases is responsible for high-affinity H2 uptake from the troposphere, and is therefore thought to play an important role in the global H2 cycle. Here we present the first crystal structure at 2.85-Å resolution of such an actinobacterial-type hydrogenase (AH), which was isolated from the dihydrogen oxidizing bacterium, Ralstonia eutropha. The enzyme has a dimeric structure carrying two active [NiFe] sites that are interconnected by six [4Fe4S] clusters over a range of approximately 90 Å. Unlike most other [NiFe]-hydrogenases, the [4Fe4S] cluster proximal to the [NiFe] site is coordinated by three cysteines and one aspartate. Mutagenesis experiments revealed that this aspartate residue is related to the apparent O2 insensitivity of the AH. Our data provide first structural insight into specialized hydrogenases that are supposed to consume atmospheric H2 under challenging conditions, i.e. at high O2 concentration and wide temperature and pH ranges.


    Organizational Affiliation

    Institut für Chemie, Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany. Electronic address: oliver.lenz@tu-berlin.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NIFE-HYDROGENASE SMALL SUBUNIT, HOFKA, B, D, F, H, L [auth M]351Cupriavidus necator H16Mutation(s): 0 
Gene Names: PHG064
EC: 1.12.99.6
UniProt
Find proteins for Q7WXQ4 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore Q7WXQ4 
Go to UniProtKB:  Q7WXQ4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NIFE-HYDROGENASE LARGE SUBUNIT, HOFGC, E, G, I, J [auth K], K [auth L]579Cupriavidus necator H16Mutation(s): 0 
Gene Names: PHG065
EC: 1.12.99.6
UniProt
Find proteins for Q7WXQ3 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore Q7WXQ3 
Go to UniProtKB:  Q7WXQ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
CA [auth F] , DA [auth F] , EA [auth F] , GA [auth H] , HA [auth H] , IA [auth H] , M [auth A] , MA [auth M] , 
CA [auth F],  DA [auth F],  EA [auth F],  GA [auth H],  HA [auth H],  IA [auth H],  M [auth A],  MA [auth M],  NA [auth M],  O [auth A],  OA [auth M],  P [auth A],  S [auth B],  T [auth B],  U [auth B],  X [auth D],  Y [auth D],  Z [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NFU
Query on NFU

Download Ideal Coordinates CCD File 
AA [auth E], FA [auth G], JA [auth I], KA [auth K], LA [auth L], V [auth C]formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download Ideal Coordinates CCD File 
BA [auth F], N [auth A], PA [auth M], Q [auth A], R [auth A], W [auth D]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.78α = 90
b = 267.971β = 106.58
c = 144.686γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references