1AYZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Authors :   D. K. Worthylake, S. Prakash, L. Prakash, C. P. Hill

Date :   12 Nov 97 (Deposition) - 26 Aug 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

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

Reference :   D. K. Worthylake, S. Prakash, L. Prakash, C. P. Hill
Crystal Structure Of The Saccharomyces Cerevisiae Ubiquitin-Conjugating Enzyme Rad6 At 2. 6 A Resolution.
J. Biol. Chem. V. 273 6271 1998
PubMed-ID: 9497353 | Reference-DOI: 10.1074/JBC.273.11.6271
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME RAD6
	Chains	:	A, B, C
	EC Number	:	6.3.2.19
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	UBC2

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1AYZ)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	NUL	UNKNOWN	CYS A:88	ACCEPTOR RESIDUE FOR ACTIVATED C-TERMINUS OF UBIQUITIN.

(no "SS Bond" information available for 1AYZ)

Asymmetric Unit

No.	Residues
1	Tyr A:63	-	Pro A:64
2	Tyr B:63	-	Pro B:64
3	Tyr C:63	-	Pro C:64

(no "SAP(SNP)/Variant" information available for 1AYZ)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC2_YEAST	7-139	3	A:7-139 B:7-139 C:7-139
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC2_YEAST	77-92	3	A:77-92 B:77-92 C:77-92

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.	UBC2_YEAST	7-139	1	A:7-139 - -
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC2_YEAST	77-92	1	A:77-92 - -

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.	UBC2_YEAST	7-139	1	- B:7-139 -
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC2_YEAST	77-92	1	- B:77-92 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC2_YEAST	7-139	1	- - C:7-139
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC2_YEAST	77-92	1	- - C:77-92

Asymmetric Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YGL058W	1	YGL058W.1	VII:393992-394510	519	UBC2_YEAST	1-172	172	3	A:2-154 B:2-154 C:2-154	153 153 153

Asymmetric Unit

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Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with UBC2_YEAST | P06104 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           UBC2_YEAST     2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
               SCOP domains d1ayza_ A: Ubiquitin conjugating enzyme, UBC                                                                                                              SCOP domains
               CATH domains 1ayzA00 A:2-154 Ubiquitin Conjugating Enzyme                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee..........eeeeeee..........eeee.................hhh.........hhhhhhhhhhhhh.........hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: A:7-139 UniProt: 7-139                                                                                    --------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-154 UniProt: 1-172 [INCOMPLETE]                                                                                                        Transcript 1
                 1ayz A   2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with UBC2_YEAST | P06104 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           UBC2_YEAST     2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
               SCOP domains d1ayzb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                              SCOP domains
               CATH domains 1ayzB00 B:2-154 Ubiquitin Conjugating Enzyme                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee..........eeeeeee..........eeee.................hhh.........hhhhhhhhhhhhh.........hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: B:7-139 UniProt: 7-139                                                                                    --------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:2-154 UniProt: 1-172 [INCOMPLETE]                                                                                                        Transcript 1
                 1ayz B   2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with UBC2_YEAST | P06104 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           UBC2_YEAST     2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
               SCOP domains d1ayzc_ C: Ubiquitin conjugating enzyme, UBC                                                                                                              SCOP domains
               CATH domains 1ayzC00 C:2-154 Ubiquitin Conjugating Enzyme                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee..........eeeeeee..........eeee.................hhh.........hhhhhhhhhhhh..........hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: C:7-139 UniProt: 7-139                                                                                    --------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:2-154 UniProt: 1-172 [INCOMPLETE]                                                                                                        Transcript 1
                 1ayz C   2 STPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMD 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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 Unit

Classes(

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Folds(

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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), ubc2 (RAD6) [TaxId: 4932] (1)

1a	d1ayza_	A:
1b	d1ayzb_	B:
1c	d1ayzc_	C:

Asymmetric 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	1ayzA00	A:2-154
1b	1ayzB00	B:2-154
1c	1ayzC00	C:2-154

(no "Pfam Domain" information available for 1AYZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (UBC2_YEAST | P06104)

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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0043142	single-stranded DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single-stranded DNA, and it drives another reaction.
	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:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006348	chromatin silencing at telomere	Repression of transcription of telomeric DNA by altering the structure of chromatin.
	GO:0000724	double-strand break repair via homologous recombination	The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
	GO:0042275	error-free postreplication DNA repair	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA via processes such as template switching, which does not remove the replication-blocking lesions but does not increase the endogenous mutation rate.
	GO:0070987	error-free translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	GO:0042276	error-prone translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
	GO:0010390	histone monoubiquitination	The modification of histones by addition of a single ubiquitin group.
	GO:0042138	meiotic DNA double-strand break formation	The cell cycle process in which double-strand breaks are generated at defined hotspots throughout the genome during meiosis I. This results in the initiation of meiotic recombination.
	GO:0031571	mitotic G1 DNA damage checkpoint	A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G1/S transition of the cell cycle in response to DNA damage.
	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.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0090089	regulation of dipeptide transport	Any process that modulates the rate, frequency or extent of dipeptide transport. Dipeptide transport is the directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0000722	telomere maintenance via recombination	Any recombinational process that contributes to the maintenance of proper telomeric length.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
	GO:0071629	ubiquitin-dependent catabolism of misfolded proteins by cytoplasm-associated proteasome	The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the cytoplasm, which are targeted to cytoplasmic proteasomes for degradation.
	GO:0071596	ubiquitin-dependent protein catabolic process via the N-end rule pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the N-end rule pathway. In the N-end rule pathway, destabilizing N-terminal residues (N-degrons) in substrates are recognized by E3 ligases (N-recognins), whereupon the substrates are linked to ubiquitin and then delivered to the proteasome for degradation.
cellular component
	GO:0033503	HULC complex	A ubiquitin-conjugating enzyme complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp1, Brl2/Rfp1 and Brl1/Rfp2.
	GO:1990304	MUB1-RAD6-UBR2 ubiquitin ligase complex	A ubiquitin ligase complex consisting of MUB1, RAD6 and UBR2 components. It ubiquitinates, and targets for destruction, the RPN4 transcription factor, which upregulates the proteasome genes. The binding of MUB1 may position the RPN4 ubiquitylation site proximal to the Ubiquitin-RAD6 thioester and allow the transfer of Ubiquitin from RAD6 to RPN4. One of its components, MUB1, is a short-lived protein ubiquitinated by the UBR2-RAD6 ubiquitin conjugating enzyme.
	GO:0097505	Rad6-Rad18 complex	A ubiquitin ligase complex found to be involved in post-replicative bypass of UV-damaged DNA and UV mutagenesis. In S. cerevisiae, the complex contains the ubiquitin conjugating enzyme Rad6 and Rad18, a protein containing a RING finger motif and a nucleotide binding motif. The yeast Rad6-Rad18 heterodimer has ubiquitin conjugating activity, binds single-stranded DNA, and possesses single-stranded DNA-dependent ATPase activity.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0000502	proteasome complex	A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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