1YQ3

Avian respiratory complex ii with oxaloacetate and ubiquinone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme

Huang, L., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.

(2006) J Biol Chem 281: 5965-5972

  • DOI: https://doi.org/10.1074/jbc.M511270200
  • Primary Citation of Related Structures:  
    1YQ3, 1YQ4, 2FBW

  • PubMed Abstract: 

    • We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site ...

    We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.

    Related Citations: 
    • Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
      Huang, L.S., Borders, T.M., Shen, J.T., Wang, C.J., Berry, E.A.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 380
    • Crystal structure of mitochondrial respiratory membrane protein complex II.
      Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.
      (2005) Cell 121: 1043
    Organizational Affiliation: 

    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoprotein subunit621Gallus gallusMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT1 (Gallus gallus)
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Go to UniProtKB:  Q9YHT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT1
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
succinate dehydrogenase Ip subunit252Gallus gallusMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT2 (Gallus gallus)
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Go to UniProtKB:  Q9YHT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT2
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT141Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for D0VWW3 (Gallus gallus)
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Entity Groups  
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UniProt GroupD0VWW3
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT103Gallus gallusMutation(s): 0 
Gene Names: SDHD, RCJMB04_23p7
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q5ZIS0 (Gallus gallus)
Explore Q5ZIS0 
Go to UniProtKB:  Q5ZIS0
Entity Groups  
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UniProt GroupQ5ZIS0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQ
Query on UQ
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Y [auth B]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N		 Ligand Interaction
FAD
Query on FAD
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E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
PEE
Query on PEE
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IA [auth C],
NA [auth D]		1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
HA [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
W [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
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X [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
JZR
Query on JZR
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GA [auth C]hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N		 Ligand Interaction
FES
Query on FES
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V [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
TEO
Query on TEO
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F [auth A]MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L		 Ligand Interaction
GOL
Query on GOL
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FA [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
U [auth A],
Z [auth B]
Unknown ligand
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.008α = 90
b = 84.398β = 90
c = 289.496γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Non-polymer description
  • Version 1.4: 2016-02-17
    Changes: Non-polymer description
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2023-08-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary