1JBB - JenaLib

Title :   UBIQUITIN CONJUGATING ENZYME, UBC13

Authors :   A. P. Vandemark, R. M. Hofmann, C. Tsui, C. M. Pickart, C. Wolberger

Date :   03 Jun 01 (Deposition) - 20 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ubiquitin, Ubiquitin-Conjugating Enzyme, E2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Vandemark, R. M. Hofmann, C. Tsui, C. M. Pickart, C. Wolberger
Molecular Insights Into Polyubiquitin Chain Assembly: Crystal Structure Of The Mms2/Ubc13 Heterodimer.
Cell(Cambridge, Mass. ) V. 105 711 2001
PubMed-ID: 11440714 | Reference-DOI: 10.1016/S0092-8674(01)00387-7
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC13_YEAST	6-138	2	A:6-138 B:6-138
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC13_YEAST	76-91	2	A:76-91 B:76-91

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC13_YEAST	6-138	1	A:6-138 -
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC13_YEAST	76-91	1	A:76-91 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC13_YEAST	6-138	1	- B:6-138
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC13_YEAST	76-91	1	- B:76-91

Exons (2, 4)

Sequences/Alignments

Asymmetric 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

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:148
 aligned with UBC13_YEAST | P52490 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
          UBC13_YEAST     3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAKK 150
               SCOP domains d1jbba_ A: Ubiquitin conjugating enzyme, UBC                                                                                                         SCOP domains
               CATH domains 1jbbA00 A:3-150 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: A:6-138 UniProt: 6-138                                                                                    ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1Exon 1.2  PDB: A:11-150 UniProt: 11-153 [INCOMPLETE]                                                                                         Transcript 1
                 1jbb A   3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAKK 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with UBC13_YEAST | P52490 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
          UBC13_YEAST     3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAK 149
               SCOP domains d1jbbb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains 1jbbB00 B:3-149 Ubiquitin Conjugating Enzyme                                                                                                        CATH domains
           Pfam domains (1) ----UQ_con-1jbbB01 B:7-144                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) ----UQ_con-1jbbB02 B:7-144                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: B:6-138 UniProt: 6-138                                                                                    ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1Exon 1.2  PDB: B:11-149 UniProt: 11-153 [INCOMPLETE]                                                                                        Transcript 1
                 1jbb B   3 SLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAK 149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A,B (UBC13_YEAST | P52490)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0010994	free ubiquitin chain polymerization	The process of creating free ubiquitin chains, compounds composed of a large number of ubiquitin monomers. These chains are not conjugated to a protein.
	GO:0006301	postreplication repair	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
	GO:0070534	protein K63-linked ubiquitination	A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
	GO:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a protein.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0031371	ubiquitin conjugating enzyme complex	Any complex that possesses ubiquitin conjugating enzyme activity.

Visualization

Interactive Views

Asymmetric Unit
	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 1jbb)

	Sites
(no "Sites" information available for 1jbb)

	Cis Peptide Bonds
		Tyr A:62 - Pro A:63	[ RasMol ]
		Tyr B:62 - Pro B:63	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1jbb
		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
	UBC13_YEAST \| P52490
		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)
	6.3.2.19
		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

Description