IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex. How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex. J. Biol. Chem. (0021-9258) 2006 imex curation Ciszak EM., Makal A., Hong YS., Vettaikkorumakankauv AK., Korotchkina LG., Patel MS. BioCreative - Critical Assessment of Information Extraction systems in Biology A construct of the didomain containing the lipoyl and E3-binding domains of E3BP (E3BPdd) without the inner domain was used to allow for mapping of interactions with E3. The three-dimensional structure of the subcomplex was determined by x-ray crystallography using a combination of molecular replacement for the elucidation of the E3 structure and de novo building of the E3BPdd structure based on the phases obtained from the E3 content. ciszakE@uah.edu 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Ciszak EM., Makal A., Hong YS., Vettaikkorumakankauv AK., Korotchkina LG., Patel MS. BioCreative - Critical Assessment of Information Extraction systems in Biology A construct of the didomain containing the lipoyl and E3-binding domains of E3BP (E3BPdd) without the inner domain was used to allow for mapping of interactions with E3. The three-dimensional structure of the subcomplex was determined by x-ray crystallography using a combination of molecular replacement for the elucidation of the E3 structure and de novo building of the E3BPdd structure based on the phases obtained from the E3 content. ciszakE@uah.edu Accepted 2006-AUG-31 by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation dldh_human Dihydrolipoyl dehydrogenase, mitochondrial DLD GCSL LAD PHE3 Dihydrolipoamide dehydrogenase Glycine cleavage system L protein protein protein human Homo sapiens Human MQSWSRVYCSLAKRGHFNRISHGLQGLSAVPLRTYADQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGGIAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEVTPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHPTLSEAFREANLAASFGKSINF This sequence has been withdrawn from Uniprot. 7613492C516F3835 7613492C516F3835 odpx_human Pyruvate dehydrogenase protein X component, mitochondrial Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex Lipoyl-containing pyruvate dehydrogenase complex component X E3-binding protein proX PDHX PDX1 protein protein human Homo sapiens Human MAASWRLGCDPRLLRYLVGFPGRRSVGLVKGALGWSVSRGANWRWFHSTQWLRGDPIKILMPSLSPTMEEGNIVKWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSKNIRLGSLIGLIVEEGEDWKHVEIPKDVGPPPPVSKPSEPRPSPEPQISIPVKKEHIPGTLRFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKITESRPTPAPTATPTAPSPLQATAGPSYPRPVIPPVSTPGQPNAVGTFTEIPASNIRRVIAKRLTESKSTVPHAYATADCDLGAVLKVRQDLVKDDIKVSVNDFIIKAAAVTLKQMPDVNVSWDGEGPKQLPFIDISVAVATDKGLLTPIIKDAAAKGIQEIADSVKALSKKARDGKLLPEEYQGGSFSISNLGMFGIDEFTAVINPPQACILAVGRFRPVLKLTEDEEGNAKLQQRQLITVTMSSDSRVVDDELATRFLKSFKANLENPIRLA DIP protein O00330 original sequence version: 174 DIP protein O00330 original sequence version: 63 9CF0C1DAE9E12EF9 dldh-pdhx 1 2 unspecified role unspecified role neutral component neutral component asp444 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain his348 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp447 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain glu437 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr438 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp413 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain glu443 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain val437 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain gly439 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain his348 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp444 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr438 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain 3 unspecified role unspecified role neutral component neutral component ser132 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain pro133 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain ala134 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asn137 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain pro154 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain arg155 binding region binding-associated region binding region western blot western blot Immuno blot Immuno blot certain certain sequence position certain certain certain sequence position certain ile157 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain lys160 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain arg136 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain glu140 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain arg155 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain pro154 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain lys160 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain pro133 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain arg136 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain glu140 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain arg155 binding region binding-associated region binding region western blot western blot Immuno blot Immuno blot certain certain sequence position certain certain certain sequence position certain arg155 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain pro133 binding region binding-associated region binding region western blot western blot Immuno blot Immuno blot certain certain sequence position certain certain certain sequence position certain 2 unspecified role unspecified role neutral component neutral component glu437 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp444 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp447 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr438 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp413 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain glu443 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain his438 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain val437 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain gly439 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain asp444 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp444 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr438 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain tyr438 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain asp447 binding region binding-associated region binding region x-ray diffraction x-ray crystallography X-ray x-ray diffraction X-ray certain certain sequence position certain certain certain sequence position certain 34 7 9 27 10 33 35 13 36 14 28 15 16 29 37 17 19 41 20 49 50 21 42 22 40 23 51 24 25 52 26 44 31 43 32 45 53 38 direct interaction direct interaction The crystalline subcomplex was obtained from the solution containing both proteins at a subunit molar ratio of 2:1, thus corresponding to one E3 (DLD, UniProt accession number P09622) dimer/E3BPdd (PDHX, UniProt accession number O00330) molecule. R working = 20.8% R free = 27.5% 2.6 Angstroms Figure 3 Table 2 In this study, we characterized binding of human E3 to the E3-binding domain of E3BP by x-ray crystallography at 2.6-A˚ resolution, and we used this structural information to interpret the specificity for selective binding. Two subunits of E3 form a single recognition site for the E3-binding domain of E3BP through their hydrophobic interface. The hydrophobic residues Pro133, Pro154, and Ile157 in the E3-binding domain of E3BP insert themselves into the surface of both E3 polypeptide chains. Numerous ionic and hydrogen bonds between the residues of three interacting polypeptide chains adjacent to the central hydrophobic patch add to the stability of the subcomplex.