1Y8X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR RECRUITMENT OF UBC12 BY AN E2-BINDING DOMAIN IN NEDD8'S E1

Authors :   D. T. Huang, A. Paydar, M. Zhuang, M. B. Waddell, J. M. Holton, B. A. Schulman

Date :   13 Dec 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   D. T. Huang, A. Paydar, M. Zhuang, M. B. Waddell, J. M. Holton, B. A. Schulman
Structural Basis For Recruitment Of Ubc12 By An E2 Binding Domain In Nedd8'S E1.
Mol. Cell V. 17 341 2005
PubMed-ID: 15694336 | Reference-DOI: 10.1016/J.MOLCEL.2004.12.020
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 M
	Chains	:	A
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBE2M, UBC12
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITIN-PROTEIN LIGASE M, UBIQUITIN CARRIER PROTEIN M, NEDD8-CONJUGATING ENZYME UBC12

Molecule 2 - UBIQUITIN-ACTIVATING ENZYME E1C
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBE1C, UBA3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEDD8-ACTIVATING ENZYME E1C, UBIQUITIN-ACTIVATING ENZYME 3 HOMOLOG

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1Y8X)

(no "SS Bond" information available for 1Y8X)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:86	-	Pro A:87

(no "SAP(SNP)/Variant" information available for 1Y8X)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC12_HUMAN	32-162	1	A:32-162
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC12_HUMAN	100-115	1	A:100-115

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000253023	1	ENSE00000892667	chr19:59070343-59069640	704	UBC12_HUMAN	1-37	37	1	A:24-37 (gaps)	16
1.2	ENST00000253023	2	ENSE00000655803	chr19:59068524-59068430	95	UBC12_HUMAN	37-68	32	1	A:37-68	32
1.3	ENST00000253023	3	ENSE00000655805	chr19:59068297-59068259	39	UBC12_HUMAN	69-81	13	1	A:69-81	13
1.4	ENST00000253023	4	ENSE00000655806	chr19:59068157-59068054	104	UBC12_HUMAN	82-116	35	1	A:82-116	35
1.5	ENST00000253023	5	ENSE00000655807	chr19:59067746-59067683	64	UBC12_HUMAN	116-137	22	1	A:116-137	22
1.6	ENST00000253023	6	ENSE00000892668	chr19:59067596-59067080	517	UBC12_HUMAN	138-183	46	1	A:138-183	46

2.1a	ENST00000361055	1a	ENSE00001864869	chr3:69129559-69129485	75	UBA3_HUMAN	1-7	7	0	-	-
2.2a	ENST00000361055	2a	ENSE00001417479	chr3:69129304-69129263	42	UBA3_HUMAN	7-21	15	0	-	-
2.3a	ENST00000361055	3a	ENSE00000966869	chr3:69127069-69126949	121	UBA3_HUMAN	21-61	41	0	-	-
2.4a	ENST00000361055	4a	ENSE00001377164	chr3:69124661-69124581	81	UBA3_HUMAN	62-88	27	0	-	-
2.5a	ENST00000361055	5a	ENSE00001376644	chr3:69120768-69120686	83	UBA3_HUMAN	89-116	28	0	-	-
2.6	ENST00000361055	6	ENSE00000966872	chr3:69117159-69117079	81	UBA3_HUMAN	116-143	28	0	-	-
2.7a	ENST00000361055	7a	ENSE00000966873	chr3:69113262-69113219	44	UBA3_HUMAN	143-158	16	0	-	-
2.8	ENST00000361055	8	ENSE00000966874	chr3:69112654-69112590	65	UBA3_HUMAN	158-179	22	0	-	-
2.9	ENST00000361055	9	ENSE00000966875	chr3:69112288-69112133	156	UBA3_HUMAN	180-231	52	0	-	-
2.10	ENST00000361055	10	ENSE00000966876	chr3:69111330-69111228	103	UBA3_HUMAN	232-266	35	0	-	-
2.11a	ENST00000361055	11a	ENSE00000966877	chr3:69111078-69110965	114	UBA3_HUMAN	266-304	39	0	-	-
2.12	ENST00000361055	12	ENSE00000966878	chr3:69106460-69106407	54	UBA3_HUMAN	304-322	19	0	-	-
2.13	ENST00000361055	13	ENSE00001656120	chr3:69105966-69105930	37	UBA3_HUMAN	322-334	13	0	-	-
2.14	ENST00000361055	14	ENSE00001685710	chr3:69105844-69105763	82	UBA3_HUMAN	334-361	28	0	-	-
2.15	ENST00000361055	15	ENSE00001754233	chr3:69105434-69105334	101	UBA3_HUMAN	362-395	34	1	B:349-374	26
2.16	ENST00000361055	16	ENSE00001711956	chr3:69105214-69105151	64	UBA3_HUMAN	395-416	22	1	B:374-395	22
2.17	ENST00000361055	17	ENSE00001673741	chr3:69105056-69105002	55	UBA3_HUMAN	417-435	19	1	B:396-414	19
2.18b	ENST00000361055	18b	ENSE00001518240	chr3:69104676-69103881	796	UBA3_HUMAN	435-463	29	1	B:414-440	27

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
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Chain A from PDB  Type:PROTEIN  Length:160
 aligned with UBC12_HUMAN | P61081 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:162
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
          UBC12_HUMAN    22 GSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIDLEGNVCLNILREDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK 183
               SCOP domains -----d1y8xa1 A:27-183 Ubiquitin conjugating enzyme, UBC                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------UQ_con-1y8xA01 A:33-168                                                                                                                 --------------- Pfam domains
         Sec.struct. author ..--..hhhhhhhhhhhhh......eeee........eeeeee...........eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhheee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------UBIQUITIN_CONJUGAT_2  PDB: A:32-162 UniProt: 32-162                                                                                --------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1        -------------------------------Exon 1.3     Exon 1.4  PDB: A:82-116            ---------------------Exon 1.6  PDB: A:138-183 UniProt: 138-183      Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.2  PDB: A:37-68          -----------------------------------------------Exon 1.5              ---------------------------------------------- Transcript 1 (2)
                 1y8x A  24 GS--mASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETmVYHPNIDLEGNVCLNILREDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSmRGGYIGSTYFERCLK 183
                             |  |   31        41        51        61        71        81        91      |101       111       121       131       141       151       161      |171       181  
                            25  |                                                                      98-MSE                                                               168-MSE           
                               26-MSE

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:92
                                   379       389       399       409       419       429       439       449       459  
           UBA3_HUMAN   370 LPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHF 461
               SCOP domains d1y8xb1 B:349-440 UBA3                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----E2_bind-1y8xB01 B:353-440                                                                Pfam domains
         Sec.struct. author ....ee.....hhhhhhhhhhhh........eeeeee..eeeeee...hhhhhhhhhhhhhh.hhhhh.....eeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.15  PDB: B:349-374 ---------------------Exon 2.17          -------------------------- Transcript 2 (1)
           Transcript 2 (2) -------------------------Exon 2.16             ------------------Exon 2.18b  PDB: B:414-440  Transcript 2 (2)
                 1y8x B 349 LPQNIQFSPSAKLQEVLDYLTNSASLQmKSPAITATLEGKNRTLYmQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHF 440
                                   358       368       378       388     | 398       408       418       428       438  
                                                     376-MSE           394-MSE

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 '\|'

(no "CATH Domain" information available for 1Y8X)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: UBC (69)

Family: UQ_con (55)

Homo sapiens (Human) (36)

UQ_con-1y8xA01

A:33-168

Clan: no clan defined [family: E2_bind] (5)

Family: E2_bind (5)

Homo sapiens (Human) (5)

E2_bind-1y8xB01

B:353-440

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UBC12_HUMAN | P61081)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019788	NEDD8 transferase activity	Catalysis of the transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y --> Y-NEDD8 + X, where both X-NEDD8 and Y-NEDD8 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: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:0018169	ribosomal S6-glutamic acid ligase activity	Catalysis of the posttranslational transfer of one or more glutamic acid residues to the C-terminus of ribosomal protein S6.
	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:0038061	NIK/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0043525	positive regulation of neuron apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
	GO:0045116	protein neddylation	Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Chain B (UBA3_HUMAN | Q8TBC4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019781	NEDD8 activating enzyme activity	Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
	GO:0016881	acid-amino acid ligase activity	Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0016922	ligand-dependent nuclear receptor binding	Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
	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: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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0008641	small protein activating enzyme activity	Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
biological process
	GO:0038061	NIK/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
	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:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0007113	endomitotic cell cycle	A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
	GO:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045116	protein neddylation	Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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
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(no "Related Entries Specified in the PDB File" available for 1Y8X)

Description

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