3RNM

The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3)

Summary for 3RNM

• Entry DOI: 10.2210/pdb3rnm/pdb
• Descriptor: Dihydrolipoyl dehydrogenase, mitochondrial, Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial, BETA-MERCAPTOETHANOL, ... (6 entities in total)
• Functional Keywords: protein-protein interaction, redox protein, mitochondrion, oxidoreductase-protein binding complex, oxidoreductase/protein binding
• Biological source: Homo sapiens (human); More
• Cellular location: Mitochondrion matrix: P09622 P11182
• Total number of polymer chains: 6
• Total formula weight: 228077.49

Authors

Brautigam, C.A.,Wynn, R.M.,Chuang, J.C.,Young, B.B.,Chuang, D.T. (deposition date: 2011-04-22, release date: 2011-05-04, Last modification date: 2025-03-26)

Primary citation

Brautigam, C.A.,Wynn, R.M.,Chuang, J.L.,Naik, M.T.,Young, B.B.,Huang, T.H.,Chuang, D.T.
Structural and Thermodynamic Basis for Weak Interactions between Dihydrolipoamide Dehydrogenase and Subunit-binding Domain of the Branched-chain {alpha}-Ketoacid Dehydrogenase Complex.
J.Biol.Chem., 286:23476-23488, 2011

PubMed Abstract: The purified mammalian branched-chain α-ketoacid dehydrogenase complex (BCKDC), which catalyzes the oxidative decarboxylation of branched-chain α-keto acids, is essentially devoid of the constituent dihydrolipoamide dehydrogenase component (E3). The absence of E3 is associated with the low affinity of the subunit-binding domain of human BCKDC (hSBDb) for hE3. In this work, sequence alignments of hSBDb with the E3-binding domain (E3BD) of the mammalian pyruvate dehydrogenase complex show that hSBDb has an arginine at position 118, where E3BD features an asparagine. Substitution of Arg-118 with an asparagine increases the binding affinity of the R118N hSBDb variant (designated hSBDb*) for hE3 by nearly 2 orders of magnitude. The enthalpy of the binding reaction changes from endothermic with the wild-type hSBDb to exothermic with the hSBDb* variant. This higher affinity interaction allowed the determination of the crystal structure of the hE3/hSBDb* complex to 2.4-Å resolution. The structure showed that the presence of Arg-118 poses a unique, possibly steric and/or electrostatic incompatibility that could impede E3 interactions with the wild-type hSBDb. Compared with the E3/E3BD structure, the hE3/hSBDb* structure has a smaller interfacial area. Solution NMR data corroborated the interactions of hE3 with Arg-118 and Asn-118 in wild-type hSBDb and mutant hSBDb*, respectively. The NMR results also showed that the interface between hSBDb and hE3 does not change significantly from hSBDb to hSBDb*. Taken together, our results represent a starting point for explaining the long standing enigma that the E2b core of the BCKDC binds E3 far more weakly relative to other α-ketoacid dehydrogenase complexes.

PubMed: 21543315
DOI: 10.1074/jbc.M110.202960

Experimental method

X-RAY DIFFRACTION (2.4 Å)