2DNC - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF RSGI RUH-054, A LIPOYL DOMAIN FROM HUMAN 2-OXOACID DEHYDROGENASE

Authors :   A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, C. Kurosaki, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   25 Apr 06 (Deposition) - 25 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Lipoic Acid, Lipoyl Domain, 2-Oxoacid Dehydrogenase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, C. Kurosaki, M. Yoshida, S. Yokoyama
Solution Structure Of Rsgi Ruh-054, A Lipoyl Domain From Human 2-Oxoacid Dehydrogenase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PYRUVATE DEHYDROGENASE PROTEIN X COMPONENT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050613-07
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN OF 2-OXOACID DEHYDROGENASES, LIPOYL BINDING DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	DIHYDROLIPOAMIDE DEHYDROGENASE-BINDING PROTEIN OF PYRUVATE DEHYDROGENASE COMPLEX, LIPOYL-CONTAINING PYRUVATE DEHYDROGENASE COMPLEX COMPONENT X, E3-BINDING PROTEIN, E3BP, PROX


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DNC)

(no "Site" information available for 2DNC)

(no "SS Bond" information available for 2DNC)

(no "Cis Peptide Bond" information available for 2DNC)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046620	T	101	A	ODPX_HUMAN	Polymorphism	11539202	A	T	52	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	ODPX_HUMAN	56-132	1	A:8-83
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	ODPX_HUMAN	81-110	1	A:32-61
3	PSBD	PS51826	Peripheral subunit-binding (PSBD) domain profile.	ODPX_HUMAN	183-220	1	A:96-98

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000227868	3a	ENSE00000824440	chr11:34938119-34938362	244	ODPX_HUMAN	1-54	54	1	A:1-7	7
1.4	ENST00000227868	4	ENSE00000710349	chr11:34952951-34953031	81	ODPX_HUMAN	54-81	28	1	A:8-32	25
1.5	ENST00000227868	5	ENSE00001150239	chr11:34969053-34969153	101	ODPX_HUMAN	81-114	34	1	A:32-65	34
1.6	ENST00000227868	6	ENSE00001150231	chr11:34978931-34979130	200	ODPX_HUMAN	115-181	67	1	A:66-95	30
1.7c	ENST00000227868	7c	ENSE00001150226	chr11:34981967-34982065	99	ODPX_HUMAN	181-214	34	1	A:96-98	3
1.8	ENST00000227868	8	ENSE00001150220	chr11:34988187-34988361	175	ODPX_HUMAN	214-272	59	0	-	-
1.9	ENST00000227868	9	ENSE00001330369	chr11:34991686-34991833	148	ODPX_HUMAN	273-322	50	0	-	-
1.11b	ENST00000227868	11b	ENSE00000710371	chr11:34999671-34999729	59	ODPX_HUMAN	322-341	20	0	-	-
1.12a	ENST00000227868	12a	ENSE00000710373	chr11:35006117-35006275	159	ODPX_HUMAN	342-394	53	0	-	-
1.13	ENST00000227868	13	ENSE00000710375	chr11:35013862-35013926	65	ODPX_HUMAN	395-416	22	0	-	-
1.14c	ENST00000227868	14c	ENSE00002154149	chr11:35016461-35017518	1058	ODPX_HUMAN	416-501	86	0	-	-

NMR Structure

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:98
 aligned with ODPX_HUMAN | O00330 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:169
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193         
           ODPX_HUMAN    34 GWSVSRGANWRWFHSTQWLRGDPIKILMPSLSPTMEEGNIVKWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSKNIRLGSLIGLIVEEGEDWKHVEIPKDVGPPPPVSKPSEPRPSPEPQISIPVKKEHIPGTLRFRLSPAARNILEKHSLDASQG 202
               SCOP domains d2dnca_                 A: automated matches                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----------------eeee.........ee.eeee......ee....eeeeee....eeeee....eeeee.........ee...eeeeee............-------------------------------------------------------... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------A----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------BIOTINYL_LIPOYL  PDB: A:8-83 UniProt: 56-132                                 --------------------------------------------------PSBD  PDB: A:96-98   PROSITE (1)
                PROSITE (2) -----------------------------------------------LIPOYL  PDB: A:32-61          -------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3a  PDB: A:1-7--------------------------Exon 1.5  PDB: A:32-65            Exon 1.6  PDB: A:66-95 UniProt: 115-181 [INCOMPLETE]               --------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.4  PDB: A:8-32       ---------------------------------------------------------------------------------------------------Exon 1.7c  PDB: A:96-9 Transcript 1 (2)
                 2dnc A   1 GSSGSSG----------------IKILMPSLSPTMEEGNIVKWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSKNIRLGSLIGLIVEEGEDWKHVSGP-------------------------------------------------------SSG  98
                                  |  -         -   |    14        24        34        44        54        64        74        84        94|        -         -         -         -         -      |  
                                  7                8                                                                                     95                                                      96

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Barrel-sandwich hybrid (185)

Superfamily: Single hybrid motif (49)

Family: automated matches (9)

Protein domain: automated matches (9)

Human (Homo sapiens) [TaxId: 9606] (2)

d2dnca_

(no "CATH Domain" information available for 2DNC)

(no "Pfam Domain" information available for 2DNC)

NMR Structure(hide GO term definitions)

Chain A (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).

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dnc)

	Sites
(no "Sites" information available for 2dnc)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dnc)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2dnc
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ODPX_HUMAN \| O00330
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ODPX_HUMAN \| O00330
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ODPX_HUMAN \| O00330	:	1zy8 2f5z 2f60

(no "Related Entries Specified in the PDB File" available for 2DNC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 3)

Exons (5, 5)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File