2L4E - JenaLib

Title :   NMR STRUCTURE OF THE UBA DOMAIN OF S. CEREVISIAE DCN1

Authors :   D. Burschowsky, F. Rudolf, D. Mattle, M. Peter, G. Wider

Date :   05 Oct 10 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Uba, Ubiquitin Binding, Neddylation, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Burschowsky, F. Rudolf, D. Mattle, M. Peter, G. Wider
Structural Analysis Of The Ubiquitin-Associated Domain (Uba Of Yeast Dcn1 In Complex With Ubiquitin
To Be Published
PubMed: search

Compounds

Molecule 1 - DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 DE3 STAR
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-4T
	Fragment	:	UBA DOMAIN (UNP RESIDUES 6-62)
	Gene	:	DCN1, DCN1 YLR128W, L3111, YLR128W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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 (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

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:57
 aligned with DCN1_YEAST | Q12395 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:57
                                    15        25        35        45        55       
            DCN1_YEAST    6 IKRKDASPEQEAIESFTSLTKCDPKVSRKYLQRNHWNINYALNDYYDKEIGTFTDEV 62
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh..hhhhhhhh..........hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:6-62 UniProt: 2-269 [INCOMPLETE]         Transcript 1
                  2l4e A  6 IKRKDASPEQEAIESFTSLTKCDPKVSRKYLQRNHWNINYALNDYYDKEIGTFTDEV 62
                                    15        25        35        45        55

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 (10, 10)

NMR Structure(hide GO term definitions)

Chain A (DCN1_YEAST | Q12395)

molecular function
	GO:0097602	cullin family protein binding	Interacting selectively and non-covalently with any member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3).
	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:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0031624	ubiquitin conjugating enzyme binding	Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins.
	GO:0032182	ubiquitin-like protein binding	Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
biological process
	GO:0051443	positive regulation of ubiquitin-protein transferase activity	Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
	GO:0045116	protein neddylation	Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0000151	ubiquitin ligase complex	A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

Visualization

Interactive Views

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 2l4e)

	Sites
(no "Sites" information available for 2l4e)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2l4e)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2l4e
		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
	DCN1_YEAST \| Q12395
		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

Analysis Tools

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
	DCN1_YEAST \| Q12395
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description