2GJD - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   DISTINCT FUNCTIONAL DOMAINS OF UBC9 DICTATE CELL SURVIVAL AND RESISTANCE TO GENOTOXIC STRESS

Authors :   R. C. Van Waardenburg, D. M. Duda, C. S. Lancaster, B. A. Schulman, M. A. Bjornsti

Date :   30 Mar 06 (Deposition) - 04 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Ubc9P, E2, Smt3, Saccharomyces Cerevisiae, Crystallography, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Van Waardenburg, D. M. Duda, C. S. Lancaster, B. A. Schulman, M. A. Bjornsti
Distinct Functional Domains Of Ubc9 Dictate Cell Survival And Resistance To Genotoxic Stress.
Mol. Cell. Biol. V. 26 4958 2006
PubMed-ID: 16782883 | Reference-DOI: 10.1128/MCB.00160-06
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2-18 KDA
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	UBC9
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	UBIQUITIN- PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2GJD)

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:68	-	Pro A:69
2	Tyr B:68	-	Pro B:69
3	Tyr C:68	-	Pro C:69
4	Tyr D:68	-	Pro D:69

(no "SAP(SNP)/Variant" information available for 2GJD)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC9_YEAST	7-146	4	A:7-146 B:7-146 C:7-146 D:7-146
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC9_YEAST	82-97	4	A:82-97 B:82-97 C:82-97 D:82-97

Asymmetric/Biological Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDL064W	1	YDL064W.1	IV:337487-337524	38	UBC9_YEAST	1-13	13	4	A:3-13 B:2-13 C:3-13 D:3-13	11 12 11 11
1.2	YDL064W	2	YDL064W.2	IV:337635-338070	436	UBC9_YEAST	13-157	145	4	A:13-157 B:13-157 C:13-157 D:13-157	145 145 145 145

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

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:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjda_ A: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdA00 A:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: A:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: A:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd A   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           UBC9_YEAST     2 SSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                                 SCOP domains
               CATH domains 2gjdB00 B:2-157 Ubiquitin Conjugating Enzyme                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: B:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1    ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: B:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd B   2 SSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdc_ C: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdC00 C:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: C:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: C:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd C   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
           UBC9_YEAST     3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
               SCOP domains d2gjdd_ D: Ubiquitin conjugating enzyme, UBC                                                                                                                SCOP domains
               CATH domains 2gjdD00 D:3-157 Ubiquitin Conjugating Enzyme                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: D:7-146 UniProt: 7-146                                                                                           ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: D:13-157 UniProt: 13-157                                                                                                           Transcript 1 (2)
                 2gjd D   3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYSK 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: UBC-related (135)

Protein domain: Ubiquitin conjugating enzyme, UBC (84)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d2gjda_	A:
1b	d2gjdb_	B:
1c	d2gjdc_	C:
1d	d2gjdd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin Conjugating Enzyme (83)

Homologous Superfamily: Ubiquitin Conjugating Enzyme (83)

Baker's yeast (Saccharomyces cerevisiae) (11)

1a	2gjdA00	A:3-157
1b	2gjdC00	C:3-157
1c	2gjdD00	D:3-157
1d	2gjdB00	B:2-157

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (UBC9_YEAST | P50623)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019789	SUMO transferase activity	Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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: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.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0000022	mitotic spindle elongation	The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	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.

Asymmetric/Biological 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 2gjd)

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

	Cis Peptide Bonds
		Tyr A:68 - Pro A:69	[ RasMol ]
		Tyr B:68 - Pro B:69	[ RasMol ]
		Tyr C:68 - Pro C:69	[ RasMol ]
		Tyr D:68 - Pro D:69	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	2gjd
		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
	UBC9_YEAST \| P50623
		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

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
	UBC9_YEAST \| P50623
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	UBC9_YEAST \| P50623	:	2eke 3ong 5jne

1a3s	CRYSTAL STRUCTURE OF HUMAN UBC9
1u9a	CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (2, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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