3O2U - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   S. CEREVISIAE UBC12

Authors :   D. C. Scott, J. K Monda, C. R. R. Grace, D. M. Duda, R. W. Kriwacki, T. Kurz B. A. Schulman

Date :   22 Jul 10 (Deposition) - 15 Sep 10 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   E2 Conjugase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. C. Scott, J. K. Monda, C. R. Grace, D. M. Duda, R. W. Kriwacki, T. Kurz, B. A. Schulman
A Dual E3 Mechanism For Rub1 Ligation To Cdc53.
Mol. Cell V. 39 784 2010
PubMed-ID: 20832729 | Reference-DOI: 10.1016/J.MOLCEL.2010.08.030

Molecule 1 - NEDD8-CONJUGATING ENZYME UBC12
	Chains	:	A, B
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBC12, YLR306W, L2142.3
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	RUB1-CONJUGATING ENZYME, RUB1-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN 12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:1033 , ASP A:1037 , SER A:1052 , PRO A:1053 , ASP A:1054	BINDING SITE FOR RESIDUE GOL A 3968
2	AC2	SOFTWARE	HOH B:117 , PRO B:1095 , LYS B:1096 , VAL B:1097 , ASN B:1113 , VAL B:1114	BINDING SITE FOR RESIDUE GOL B 3968

(no "SS Bond" information available for 3O2U)

Asymmetric Unit

No.	Residues
1	Tyr A:1090	-	Pro A:1091
2	Ser A:1187	-	Pro A:1188
3	Tyr B:1090	-	Pro B:1091

(no "SAP(SNP)/Variant" information available for 3O2U)

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.	UBC12_YEAST	30-166	2	A:1030-1166 B:1030-1166
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC12_YEAST	104-119	2	A:1104-1119 B:1104-1119

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.	UBC12_YEAST	30-166	1	A:1030-1166 -
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC12_YEAST	104-119	1	A:1104-1119 -

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.	UBC12_YEAST	30-166	1	- B:1030-1166
2	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC12_YEAST	104-119	1	- B:1104-1119

(no "Exon" information available for 3O2U)

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:190
 aligned with UBC12_YEAST | P52491 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:190
                              1                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
         UBC12_YEAST      - --MLKLRQLQKKKQKENENSSSIQPNLSAARIRLKRDLDSLDLPPTVTLNVITSPDSADRSQSPKLEVIVRPDEGYYNYGSINFNLDFNEVYPIEPPKVVCLKKIFHPNIDLKGNVCLNILREDWSPALDLQSIITGLLFLFLEPNPNDPLNKDAAKLLCEGEKEFAEAVRLTMSGGSIEHVKYDNIVSP  188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......eeeeeee...........eeeeee...........eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..ee..ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------UBIQUITIN_CONJUGAT_2  PDB: A:1030-1166 UniProt: 30-166                                                                                   ---------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o2u A  999 GSMLKLRQLQKKKQKENENSSSIQPNLSAARIRLKRDLDSLDLPPTVTLNVITSPDSADRSQSPKLEVIVRPDEGYYNYGSINFNLDFNEVYPIEPPKVVCLKKIFHPNIDLKGNVCLNILREDWSPALDLQSIITGLLFLFLEPNPNDPLNKDAAKLLCEGEKEFAEAVRLTMSGGSIEHVKYDNIVSP 1188
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with UBC12_YEAST | P52491 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
         UBC12_YEAST      2 LKLRQLQKKKQKENENSSSIQPNLSAARIRLKRDLDSLDLPPTVTLNVITSPDSADRSQSPKLEVIVRPDEGYYNYGSINFNLDFNEVYPIEPPKVVCLKKIFHPNIDLKGNVCLNILREDWSPALDLQSIITGLLFLFLEPNPNDPLNKDAAKLLCEGEKEFAEAVRLTMSGGSIEHVKYDNIVSP  188
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------UQ_con-3o2uB01 B:1031-1172                                                                                                                    ---------------- Pfam domains (1)
           Pfam domains (2) -----------------------------UQ_con-3o2uB02 B:1031-1172                                                                                                                    ---------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh.--...hhhhhhhhhhhhh......eeeeeee...........eeeeee...........eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..ee..ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------UBIQUITIN_CONJUGAT_2  PDB: B:1030-1166 UniProt: 30-166                                                                                   ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o2u B 1002 LKLRQLQKKKQKENENSSS--PNLSAARIRLKRDLDSLDLPPTVTLNVITSPDSADRSQSPKLEVIVRPDEGYYNYGSINFNLDFNEVYPIEPPKVVCLKKIFHPNIDLKGNVCLNILREDWSPALDLQSIITGLLFLFLEPNPNDPLNKDAAKLLCEGEKEFAEAVRLTMSGGSIEHVKYDNIVSP 1188
                                  1011        |- |    1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181       
                                           1020  |                                                                                                                                                                     
                                              1023

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 "SCOP Domain" information available for 3O2U)

(no "CATH Domain" information available for 3O2U)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: UBC (69)

Family: UQ_con (55)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (6)

1a	UQ_con-3o2uB01	B:1031-1172
1b	UQ_con-3o2uB02	B:1031-1172

Asymmetric Unit(hide GO term definitions)

Chain A,B (UBC12_YEAST | P52491)

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: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:0045116	protein neddylation	Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:1187 - Pro A:1188	[ RasMol ]
		Tyr A:1090 - Pro A:1091	[ RasMol ]
		Tyr B:1090 - Pro B:1091	[ RasMol ]

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

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Access by PDB/NDB ID
	3o2u
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	UBC12_YEAST \| P52491
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	6.3.2.-
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	UBC12_YEAST \| P52491
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	UBC12_YEAST \| P52491	:	3tdi

3o2p	E3-SUBSTRATE
3o6b	E2 E3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Gene Ontology (9, 9)

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