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Overview for MACiE Entry M0294

Version history

General Information

EC Number: 1.3.5.1 (A member of the Oxidoreductases, Acting on the CH-CH group of donors, With a quinone or related compound as acceptor)

Enzyme Name: succinate dehydrogenase (ubiquinone)

Biological Species: Gallus gallus (Chicken)

Catalytic Chain UniprotKB Accession Codes:

  • Q9YHT1 - Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Representative PDB Code: 1yq4 - AVIAN RESPIRATORY COMPLEX II WITH 3-NITROPROPIONATE AND UBIQUINONE (Resolution = 2.33 Å).

Catalytic CATH Codes:

  • 3.50.50.60 - FAD/NAD(P)-binding domain
  • Unassigned Domain

"Other" CATH Codes:

  • 1.10.1060.10 - Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
  • 1.20.5.540 - Single helix bin
  • 1.20.58.100 - Methane Monooxygenase Hydroxylase; Chain G, domain 1
  • 3.10.20.30 - Ubiquitin-like (UB roll)
  • 1.20.1300.10 - Fumarate reductase respiratory complex transmembrane subunits
  • 4.10.80.40 - succinate dehydrogenase protein domain

Display structure information

Overall Reaction:

Image of ubiquniol

Image of fumarate

right arrow

Image of ubiquinone

Image of succinate

ubiquniol
C00390
CHEBI:17976
fumarate
C00122
CHEBI:37154
ubiquinone
C00399
CHEBI:16389
succinate
C00042
CHEBI:30031

This reaction is irreversible.

Overall Comment: The two small membrane anchor subunits ligate a single, low spin cytochrome b heme group. In the yeast homologue, the heme groups has been shown not to be involved in the electron transport mechanism between the active site and the ubiquinol binding site [5].


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Stepwise Description of the Reaction

Step 1Ubiquinol acts as a two electron donor to the FAD cofactor, forming anionic FADH.
Step 2The FADH N5 acts as a hydride donor to the polarised double bond in fumarate. A proton is simultaneously abstracted from Arg297 to saturate the double bond, forming succinate.
Step 3The catalytic acid/base is reprotonated by a solvent molecule.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Phe 130 A Side Chain
Leu 263 A Side Chain
Glu 266 A Side Chain
Gln 251 A Side Chain
His 253 A Side Chain
His 364 A Side Chain
Arg 408 A Side Chain
Arg 297 A Side Chain

Organic Cofactors for M0294

Type Identity Chain
FAD FAD 1001 A Overview

Metal Cofactors for M0294

Type Het group Number Chain
iron SF4 1003 B Overview
iron F3S 1004 B Overview
iron No Available PDB Information

References

  1. L. S. Huang et al. (2005), J. Biol. Chem., 281, 5965-5972. 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.
    Medline: 16371358
  2. C. G. Mowat et al. (2001), Biochemistry, 40, 12292-12298. Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase.
    Medline: 11591148
  3. P. Taylor et al. (1999), Nat. Struct. Biol., 6, 1108-1112. Structural and mechanistic mapping of a unique fumarate reductase.
    Medline: 10581550
  4. J. Zhang et al. (2006), Proc. Natl Acad. Sci. USA, 103, 16212-16217. Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
    Medline: 17050691
  5. K. S. Oyedotun et al. (2007), Biochim. Biophys. Acta, 1767, 1436-1445. The Saccharomyces cerevisiae succinate dehydrogenase does not require heme for ubiquinone reduction.
    Medline: 18028869
  6. R. Horsefield et al. (2005), J. Bio. Chem., 281, 7308-7316. Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction.
    Medline: 16407191

Homologue information for M0294 (1yq4)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0020 succinate dehydrogenase
1.3.99.1
1qjd 3.50.50.60
0.0.0.0
0.43820.6892Compare
M0113 sarcosine oxidase
1.5.3.1
2gb0 3.50.50.60
0.29660.1058Compare
M0006 glutathione-disulfide reductase
1.8.1.7
2gh5 3.50.50.60
0.40780.2098Compare
M0123 adenylyl-sulfate reductase
1.8.99.2
1jnr 3.50.50.60
1.20.58.100
0.250.2646Compare
M0131 4-hydroxybenzoate 3-monooxygenase
1.14.13.2
1doc 3.50.50.60
0.0530.1058Compare
M0142 ferredoxin-NADP+ reductase
1.18.1.2
1e6e 3.50.50.60
3.10.20.30
0.42850.1411Compare

View a comparison of the other reactions in MACiE with the CATH domain 0.0.0.0

View a comparison of the other reactions in MACiE with the CATH domain 3.10.20.30

View a comparison of the other reactions in MACiE with the CATH domain 3.50.50.60


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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succinate dehydrogenase activity (molecular function)
iron ion binding (molecular function)
mitochondrion (cellular component)
mitochondrial envelope (cellular component)
mitochondrial inner membrane (cellular component)
mitochondrial respiratory chain complex II (cellular component)
tricarboxylic acid cycle (biological process)
succinate metabolic process (biological process)
transport (biological process)
nervous system development (biological process)
succinate dehydrogenase (ubiquinone) activity (molecular function)
electron carrier activity (molecular function)
membrane (cellular component)
integral component of membrane (cellular component)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on the CH-CH group of donors (molecular function)
heme binding (molecular function)
electron transport chain (biological process)
respiratory electron transport chain (biological process)
flavin adenine dinucleotide binding (molecular function)
iron-sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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