6QPX

Crystal structure of nitrite bound Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis.

Hedison, T.M., Shenoy, R.T., Iorgu, A.I., Heyes, D.J., Fisher, K., Wright, G.S.A., Hay, S., Eady, R.R., Antonyuk, S.V., Hasnain, S.S., Scrutton, N.S.

(2019) ACS Catal 9: 6087-6099

  • DOI: 10.1021/acscatal.9b01266
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • It is generally assumed that tethering enhances rates of electron harvesting and delivery to active sites in multidomain enzymes by proximity and sampling mechanisms. Here, we explore this idea in a tethered 3-domain, trimeric copper-containing nitrite reductase ...

    It is generally assumed that tethering enhances rates of electron harvesting and delivery to active sites in multidomain enzymes by proximity and sampling mechanisms. Here, we explore this idea in a tethered 3-domain, trimeric copper-containing nitrite reductase. By reverse engineering, we find that tethering does not enhance the rate of electron delivery from its pendant cytochrome c to the catalytic copper-containing core. Using a linker that harbors a gatekeeper tyrosine in a nitrite access channel, the tethered haem domain enables catalysis by other mechanisms. Tethering communicates the redox state of the haem to the distant T2Cu center that helps initiate substrate binding for catalysis. It also tunes copper reduction potentials, suppresses reductive enzyme inactivation, enhances enzyme affinity for substrate, and promotes intercopper electron transfer. Tethering has multiple unanticipated beneficial roles, the combination of which fine-tunes function beyond simplistic mechanisms expected from proximity and restrictive sampling models.

    Organizational Affiliation: 

    Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-containing nitrite reductaseA, I468Ralstonia pickettiiMutation(s): 1 
Gene Names: HMPREF0989_00586
EC: 1.7.2.1
Find proteins for I6NAW4 (Ralstonia pickettii)
Explore I6NAW4 
Go to UniProtKB:  I6NAW4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC
Download CCD File 
A, I
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
CU
Query on CU
Download CCD File 
A, I
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
NO2
Query on NO2
Download CCD File 
A, I
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.5α = 90
b = 128.5β = 90
c = 172.47γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N019380/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N013972/1

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references