5GUW

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dynamics of nitric oxide controlled by protein complex in bacterial system

Terasaka, E.Yamada, K.Wang, P.H.Hosokawa, K.Yamagiwa, R.Matsumoto, K.Ishii, S.Mori, T.Yagi, K.Sawai, H.Arai, H.Sugimoto, H.Sugita, Y.Shiro, Y.Tosha, T.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 9888-9893

  • DOI: 10.1073/pnas.1621301114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system ...

    Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-Å resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO.


    Related Citations: 
    • Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
      Sato, N.,Ishii, S.,Sugimoto, H.,Hino, T.,Fukumori, Y.,Sako, Y.,Shiro, Y.,Tosha, T.
      (2014) Proteins 82: 1258
    • Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
      Matsumoto, Y.,Tosha, T.,Pisliakov, A.V.,Hino, T.,Sugimoto, H.,Nagano, S.,Sugita, Y.,Shiro, Y.
      (2012) Nat. Struct. Mol. Biol. 19: 238
    • Structural basis of biological N2O generation by bacterial nitric oxide reductase.
      Hino, T.,Matsumoto, Y.,Nagano, S.,Sugimoto, H.,Fukumori, Y.,Murata, T.,Iwata, S.,Shiro, Y.
      (2010) Science 330: 1666


    Organizational Affiliation

    Biometal Science Laboratory, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide reductase subunit C
A, C
146Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: norC
Find proteins for Q59646 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q59646
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide reductase subunit B
B, D
465Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: norB
EC: 1.7.2.5
Find proteins for Q59647 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q59647
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nitrite reductase
M, N
568Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: nirS
EC: 1.7.2.1
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P24474
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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M, N
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

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B, D
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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B, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

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B, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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A, C, M, N
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
10M
Query on 10M

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A, C, D
decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
(2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-Decylsulfanyl-4,5-dihydroxy-2-hydroxymethyl-tetrahydro-pyran-3-yloxy)-6-hydroxymethyl-tetrahydro-pyran-3,4,5-triol, n-Decyl-beta-D-thiomaltoside
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N
 Ligand Interaction
DHE
Query on DHE

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M, N
HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 111.871α = 90.00
b = 128.606β = 106.83
c = 127.807γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KAKENHIJapanJP26220807
KAKENHIJP26620140

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references