2Y4W - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF HUMAN UBIQUITIN CONJUGATING ENZYME RAD6B

Authors :   A. Huang, R. G. Hibbert, R. N. Dejong, D. Das, T. K. Sixma, R. Boelens

Date :   11 Jan 11 (Deposition) - 11 May 11 (Release) - 27 Jun 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Ligase, Dna Damage, Dna Repair, Ubiquitination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Huang, R. G. Hibbert, R. N. Dejong, D. Das, T. K. Sixma, R. Boelens
Symmetry And Asymmetry Of The Ring-Ring Dimer Of Rad18
J. Mol. Biol. V. 410 424 2011
PubMed-ID: 21549715 | Reference-DOI: 10.1016/J.JMB.2011.04.051

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 B
	Chains	:	A
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PLIS
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAD6 HOMOLOG B, UBIQUITIN CARRIER PROTEIN B, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA, UBIQUITIN-PROTEIN LIGASE B, HR6B, HHR6B, RAD6B

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Y4W)

(no "Site" information available for 2Y4W)

(no "SS Bond" information available for 2Y4W)

(no "Cis Peptide Bond" information available for 2Y4W)

(no "SAP(SNP)/Variant" information available for 2Y4W)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBE2B_HUMAN	7-139	1	A:7-139
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBE2B_HUMAN	77-92	1	A:77-92

NMR Structure * (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBE2B_HUMAN	7-139	1	A:7-139
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBE2B_HUMAN	77-92	1	A:77-92

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000265339	1a	ENSE00001042376	chr5:133706870-133707330	461	UBE2B_HUMAN	1-15	15	1	A:1-15	15
1.2a	ENST00000265339	2a	ENSE00000953701	chr5:133710074-133710154	81	UBE2B_HUMAN	15-42	28	1	A:15-42	28
1.3	ENST00000265339	3	ENSE00001042373	chr5:133712360-133712385	26	UBE2B_HUMAN	42-51	10	1	A:42-51	10
1.4	ENST00000265339	4	ENSE00000803566	chr5:133716410-133716499	90	UBE2B_HUMAN	51-81	31	1	A:51-81	31
1.6b	ENST00000265339	6b	ENSE00000763369	chr5:133724016-133724104	89	UBE2B_HUMAN	81-110	30	1	A:81-110	30
1.8g	ENST00000265339	8g	ENSE00000803567	chr5:133725916-133727683	1768	UBE2B_HUMAN	111-152	42	1	A:111-152	42

NMR Structure

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

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:152
 aligned with UBE2B_HUMAN | P63146 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          UBE2B_HUMAN     1 MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWNDS 152
               SCOP domains d2y4wa_ A: Ubiquitin conjugating enzyme, UBC                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------UQ_con-2y4wA01 A:8-145                                                                                                                    ------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....eeee.........eeeee..........eeeeeee..........eeee................hhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.... 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 (1) Exon 1.1a      --------------------------Exon 1.3  -----------------------------Exon 1.6b  PDB: A:81-110      Exon 1.8g  PDB: A:111-152 UniProt: 111-152 Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2a  PDB: A:15-42     --------Exon 1.4  PDB: A:51-81         ----------------------------------------------------------------------- Transcript 1 (2)
                 2y4w A   1 MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWNDS 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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: 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)

Human (Homo sapiens), ubc2b [TaxId: 9606] (4)

d2y4wa_

(no "CATH Domain" information available for 2Y4W)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: UBC (69)

Family: UQ_con (55)

Homo sapiens (Human) (36)

UQ_con-2y4wA01

A:8-145

NMR Structure(hide GO term definitions)

Chain A (UBE2B_HUMAN | P63146)

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:0061631	ubiquitin conjugating enzyme activity	Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
	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:0042769	DNA damage response, detection of DNA damage	The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
	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:0060070	canonical Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
	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:0051026	chiasma assembly	The cell cycle process in which a connection between chromatids assembles, indicating where an exchange of homologous segments has taken place by the crossing-over of non-sister chromatids.
	GO:0033522	histone H2A ubiquitination	The modification of histone H2A by addition of one or more ubiquitin groups.
	GO:0070076	histone lysine demethylation	The modification of a histone by the removal of a methyl group from a lysine residue.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0006344	maintenance of chromatin silencing	The maintenance of chromatin in a transcriptionally silent state such as heterochromatin.
	GO:0045141	meiotic telomere clustering	The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043951	negative regulation of cAMP-mediated signaling	Any process which stops, prevents, or reduces the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
	GO:0033128	negative regulation of histone phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.
	GO:0010845	positive regulation of reciprocal meiotic recombination	Any process that increases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate.
	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:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0070979	protein K11-linked ubiquitination	A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
	GO:0070936	protein K48-linked ubiquitination	A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
	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:0051865	protein autoubiquitination	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
	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:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0031056	regulation of histone modification	Any process that modulates the frequency, rate or extent of the covalent alteration of a histone.
	GO:0009411	response to UV	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007288	sperm axoneme assembly	The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0070193	synaptonemal complex organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synaptonemal complex. A synaptonemal complex is a proteinaceous scaffold formed between homologous chromosomes during meiosis.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
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:0001741	XY body	A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

NMR Structure
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	2y4w
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	UBE2B_HUMAN \| P63146	:	1jas 1nxa 2yb6 2ybf

1jas	HSUBC2B
1nxa	HOMOLOGY MODELED UBIQUITIN-PROTEIN LIGASE B
2y43	RAD18 UBIQUITIN LIGASE RING DOMAIN STRUCTURE

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Ligands, Modified Residues, Ions (0, 0)

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