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EC Number

Catalytic Site Atlas

CSA LITERATURE entry for 1d4c

E.C. namesuccinate dehydrogenase
SpeciesShewanella putrefaciens (strain CN-32 / ATCC BAA-453)
E.C. Number (IntEnz)
CSA Homologues of 1d4cThere are 36 Homologs
CSA Entries With UniProtID P83223
CSA Entries With EC Number
PDBe Entry 1d4c
PDBSum Entry 1d4c
MACiE Entry 1d4c

Literature Report

IntroductionFumarate respiration is the most commonly occurring type of anaerobic respiration. Fumarate reductases, which catalyse the interconversion of fumarate and succinate are known to be membrane bound in bacteria although soluble versions also exist in yeast, procyclic Trypanosoma brucei and several Shewanella species. The active site is located in the centre of the protein, at the interface between the three catalytic domains. Catalysis in the soluble fumarate reductase is essentially unidirectional (from fumarte to succinate).
MechansimCatalysis is initiated by twisting the C1 carboxylate group of the fumarate out of the molecular plane. The substrate carbonyl groups are polarised through interactions with surrounding charged residues, facilitating hydride transfer from N5 of reduced FAD to the substrate C2. Reprotonation at C3 by Arg401 forms the succinate product.

Catalytic Sites for 1d4c

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA503528macie:sideChainDuring the hydride transfer from the FAD cofactor to the fumarate C1, the residue stabilises the forming anionic charge on the oxygen through hydrogen bonding and subsequent proton donation. The residue is activated towards its catalytic role through interactions with His504.
ArgA401426macie:sideChainOnce hydride transfer has occurred, the residue is correctly positioned to donate a proton to the substrate C3 position, resulting in the formation of succinate. The residue is immediately reprotonated through a proton relay with Arg380 and Glu377.
ArgA544569macie:sideChainElectrostatic interactions between the anionic carboxylate group and the residue's cationic side chain twist the substrate into a reactive conformation and polarise the carboxylate carbonyl which facilitates hydride transfer to the double bond C3.
GluA377402macie:sideChainThe residue relays a proton to the general acid Arg401 from Arg380.
HisA504529macie:sideChainHis 504 modifies the pKa of the general acid His503 through hydrogen bond interactions, activating the residue towards its catalytic role.

Literature References

Pankhurst KL
Role of His505 in the soluble fumarate reductase from Shewanella frigidimarina.
Biochemistry 2002 41 8551-8556
PubMed: 12093271
Doherty MK
Identification of the active site acid/base catalyst in a bacterial fumarate reductase: a kinetic and crystallographic study.
Biochemistry 2000 39 10695-10701
PubMed: 10978153
Leys D
Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.
Nat Struct Biol 1999 6 1113-1117
PubMed: 10581551