9FEK

Crystal structure of guanidinase from Nitrospira inopinata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Growth of complete ammonia oxidizers on guanidine.

Palatinszky, M.Herbold, C.W.Sedlacek, C.J.Puhringer, D.Kitzinger, K.Giguere, A.T.Wasmund, K.Nielsen, P.H.Dueholm, M.K.D.Jehmlich, N.Gruseck, R.Legin, A.Kostan, J.Krasnici, N.Schreiner, C.Palmetzhofer, J.Hofmann, T.Zumstein, M.Djinovic-Carugo, K.Daims, H.Wagner, M.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07832-z
  • Primary Citation of Related Structures:  
    9FEK

  • PubMed Abstract: 

    Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry 1-3 . Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.


  • Organizational Affiliation

    Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative agmatinase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
384Candidatus Nitrospira inopinataMutation(s): 0 
Gene Names: speBNITINOP_1173
EC: 3.5.3.11
UniProt
Find proteins for A0A0S4KUT0 (Candidatus Nitrospira inopinata)
Explore A0A0S4KUT0 
Go to UniProtKB:  A0A0S4KUT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4KUT0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth K]
BB [auth K]
CA [auth E]
DA [auth E]
EB [auth L]
AB [auth K],
BB [auth K],
CA [auth E],
DA [auth E],
EB [auth L],
FB [auth L],
GA [auth F],
HA [auth F],
KA [auth G],
LA [auth G],
M [auth A],
N [auth A],
OA [auth H],
PA [auth H],
Q [auth B],
R [auth B],
SA [auth I],
TA [auth I],
U [auth C],
V [auth C],
WA [auth J],
XA [auth J],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
BA [auth D]
DB [auth K]
FA [auth E]
HB [auth L]
JA [auth F]
BA [auth D],
DB [auth K],
FA [auth E],
HB [auth L],
JA [auth F],
NA [auth G],
P [auth A],
RA [auth H],
T [auth B],
VA [auth I],
X [auth C],
ZA [auth J]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D]
CB [auth K]
EA [auth E]
GB [auth L]
IA [auth F]
AA [auth D],
CB [auth K],
EA [auth E],
GB [auth L],
IA [auth F],
MA [auth G],
O [auth A],
QA [auth H],
S [auth B],
UA [auth I],
W [auth C],
YA [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.965α = 90
b = 164.791β = 90.03
c = 143.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Vienna Science and Technology Fund (WWTF)AustriaFA705009
Christian Doppler ForschungsgesellschaftAustriaFA743017
University of Vienna Research Platform ComammoxAustria326300
European Regional Development FundEuropean UnionFA263001

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Database references