2F60 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE DIHYDROLIPOAMIDE DEHYDROGENASE (E3)-BINDING DOMAIN OF HUMAN E3-BINDING PROTEIN

Authors :   C. A. Brautigam, J. L. Chuang, R. M. Wynn, D. R. Tomchick, M. Machius, D. T

Date :   28 Nov 05 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym./Biol. Unit : K

Keywords :   Protein-Binding Protein, E3Bd, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Brautigam, R. M. Wynn, J. L. Chuang, M. Machius, D. R. Tomchick, D. T. Chuang
Structural Insight Into Interactions Between Dihydrolipoamide Dehydrogenase (E3) And E3 Binding Protein Of Human Pyruvate Dehydrogenase Complex.
Structure V. 14 611 2006
PubMed-ID: 16442803 | Reference-DOI: 10.1016/J.STR.2006.01.001

Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE PROTEIN X COMPONENT
	Chains	:	K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-LTE3BD
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	E3-BINDING DOMAIN, RESIDUES 173-230
	Gene	:	PDHX, PDX1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DIHYDROLIPOAMIDE DEHYDROGENASE-BINDING PROTEIN OF PYRUVATE DEHYDROGENASE COMPLEX, LIPOYL-CONTAINING PYRUVATE DEHYDROGENASE COMPLEX COMPONENT X, E3-BINDING PROTEIN, E3BP, PROX

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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Chain K from PDB  Type:PROTEIN  Length:60
 aligned with ODPX_HUMAN | O00330 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:60
                                   183       193       203       213       223       233
           ODPX_HUMAN   174 EHIPGTLRFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKITESRP 233
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------PSBD  PDB: K:130-167 UniProt: 183-220 ------------- PROSITE
           Transcript 1 (1) Exon 1.6--------------------------------Exon 1.8             Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.7c  PDB: K:128-161         ------------------- Transcript 1 (2)
                 2f60 K 121 EHIPGTLRFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKILEHHH 180
                                   130       140       150       160       170       180

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain K (ODPX_HUMAN | O00330)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0034604	pyruvate dehydrogenase (NAD+) activity	Catalysis of the reaction: pyruvate + CoA + NAD+ = acetyl-CoA + CO2 + NADH.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0046487	glyoxylate metabolic process	The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0061732	mitochondrial acetyl-CoA biosynthetic process from pyruvate	The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate in the mitochondrion. The process begins with the transport of pyruvate from the cytosol to the mitochondrion where it is subsequently decarboxylated to form acetyl-CoA.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
	GO:0010510	regulation of acetyl-CoA biosynthetic process from pyruvate	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0045254	pyruvate dehydrogenase complex	Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3).

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