5C2W

Kuenenia stuttgartiensis Hydrazine Synthase Pressurized with 20 bar Xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The inner workings of the hydrazine synthase multiprotein complex.

Dietl, A.Ferousi, C.Maalcke, W.J.Menzel, A.de Vries, S.Keltjens, J.T.Jetten, M.S.Kartal, B.Barends, T.R.

(2015) Nature 527: 394-397

  • DOI: 10.1038/nature15517
  • Primary Citation of Related Structures:  
    5C2V, 5C2W

  • PubMed Abstract: 
  • Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans ...

    Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDRAZINE SYNTHASE ALPHA SUBUNITA, D782Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: kuste2861
EC: 1.7.2.7
UniProt
Find proteins for Q1Q0T2 (Kuenenia stuttgartiensis)
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Go to UniProtKB:  Q1Q0T2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1Q0T2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HYDRAZINE SYNTHASE BETA SUBUNITB, E352Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: kuste2859
UniProt
Find proteins for Q1Q0T4 (Kuenenia stuttgartiensis)
Explore Q1Q0T4 
Go to UniProtKB:  Q1Q0T4
Entity Groups  
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UniProt GroupQ1Q0T4
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical (Di heme) proteinC, F314Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: kuste2860
EC: 1.7.2.7
UniProt
Find proteins for Q1Q0T3 (Kuenenia stuttgartiensis)
Explore Q1Q0T3 
Go to UniProtKB:  Q1Q0T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1Q0T3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
GA [auth D],
HA [auth D],
M [auth A],
N [auth A],
PA [auth F],
GA [auth D],
HA [auth D],
M [auth A],
N [auth A],
PA [auth F],
QA [auth F],
X [auth C],
Y [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
XE
Query on XE

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AA [auth D],
BA [auth D],
G [auth A],
H [auth A]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
BET
Query on BET

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IA [auth D],
LA [auth E],
O [auth A],
P [auth A],
Q [auth A],
IA [auth D],
LA [auth E],
O [auth A],
P [auth A],
Q [auth A],
T [auth B],
Z [auth C]
TRIMETHYL GLYCINE
C5 H12 N O2
KWIUHFFTVRNATP-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

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FA [auth D],
L [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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DA [auth D],
EA [auth D],
J [auth A],
K [auth A],
KA [auth E],
DA [auth D],
EA [auth D],
J [auth A],
K [auth A],
KA [auth E],
MA [auth F],
NA [auth F],
OA [auth F],
S [auth B],
U [auth C],
V [auth C],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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CA [auth D],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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JA [auth E],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 464.12α = 90
b = 464.12β = 90
c = 145.45γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references