8RFP

Low pH (5.5) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.83 MGy] - nitrite/NO intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases.

Rose, S.L.Ferroni, F.M.Horrell, S.Brondino, C.D.Eady, R.R.Jaho, S.Hough, M.A.Owen, R.L.Antonyuk, S.V.Hasnain, S.S.

(2024) J Mol Biol 436: 168706-168706

  • DOI: https://doi.org/10.1016/j.jmb.2024.168706
  • Primary Citation of Related Structures:  
    8R8S, 8RFL, 8RFO, 8RFP, 8RFQ, 8RFR, 8RFS, 8RFT, 8RFU, 8RFV, 8RFW, 8RFX, 8RFY, 8RG8, 8RG9, 8RGB, 8RGC, 8RGD, 8RU9, 8RUR, 8RYJ, 8RYR, 8RYU, 8RYV, 8S0W, 8S2Q, 8S5X, 8S5Y, 8S63, 8S64, 8S68, 8S69, 9EVM

  • PubMed Abstract: 

    Copper nitrite reductases (CuNiRs) exhibit a strong pH dependence of their catalytic activity. Structural movies can be obtained by serially recording multiple structures (frames) from the same spot of a crystal using the MSOX serial crystallography approach. This method has been combined with on-line single crystal optical spectroscopy to capture the pH-dependent structural changes that accompany during turnover of CuNiRs from two Rhizobia species. The structural movies, initiated by the redox activation of a type-1 copper site (T1Cu) via X-ray generated photoelectrons, have been obtained for the substrate-free and substrate-bound states at low (high enzymatic activity) and high (low enzymatic activity) pH. At low pH, formation of the product nitric oxide (NO) is complete at the catalytic type-2 copper site (T2Cu) after a dose of 3 MGy (frame 5) with full bleaching of the T1Cu ligand-to-metal charge transfer (LMCT) 455 nm band (S(σ) Cys → T1Cu 2+ ) which in itself indicates the electronic route of proton-coupled electron transfer (PCET) from T1Cu to T2Cu. In contrast at high pH, the changes in optical spectra are relatively small and the formation of NO is only observed in later frames (frame 15 in Br 2D NiR, 10 MGy), consistent with the loss of PCET required for catalysis. This is accompanied by decarboxylation of the catalytic Asp CAT residue, with CO 2 trapped in the catalytic pocket.


  • Organizational Affiliation

    Molecular Biophysics Group, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase340Bradyrhizobium diazoefficiens USDA 110Mutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
UniProt
Find proteins for Q89EJ6 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110))
Explore Q89EJ6 
Go to UniProtKB:  Q89EJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89EJ6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseB [auth C]2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2 (Subject of Investigation/LOI)
Query on NO2

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
NO (Subject of Investigation/LOI)
Query on NO

Download Ideal Coordinates CCD File 
H [auth A]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.21α = 90
b = 104.21β = 90
c = 64.37γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N013972/1
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)ArgentinaPICT 2020-00522

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references, Structure summary