1Z2U - JenaLib

Title :   THE 1.1A CRYSTALLOGRAPHIC STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME (UBC-2) FROM CAENORHABDITIS ELEGANS: FUNCTIONAL AND EVOLUTIONARY SIGNIFICANCE

Authors :   J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng, Southeast Collaboratory For Structural Genomics (Secsg)

Date :   09 Mar 05 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

Chains :   Asym./Biol. Unit : A

Keywords :   Psi, Secsg, Ubiquitin-Conjugating Enzyme, Caenorhabditis Elegans, Proteosome Pathway, Structural Genomics, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng
The 1. 1A Crystallographic Structure Of Ubiquitin-Conjugating Enzyme (Ubc-2) From Caenorhabditis Elegans: Functional And Evolutionary Significance
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 2
	Chains	:	A
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	UBC-2, LET-70
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	UBIQUITIN-PROTEIN LIGASE 2, UBIQUITIN CARRIER PROTEIN 2

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:58 , ASP A:59 , LYS A:63 , UNX A:502	BINDING SITE FOR RESIDUE CL A 601
02	AC2	SOFTWARE	SER A:-1 , ARG A:131 , LYS A:144 , HOH A:318	BINDING SITE FOR RESIDUE CL A 602
03	AC3	SOFTWARE	HIS A:0 , LEU A:3 , ARG A:131 , HOH A:315 , HOH A:356	BINDING SITE FOR RESIDUE CL A 603
04	AC4	SOFTWARE	ARG A:15	BINDING SITE FOR RESIDUE CL A 604
05	AC5	SOFTWARE	GLY A:-2 , HIS A:0 , LYS A:4 , MET A:147	BINDING SITE FOR RESIDUE CL A 605
06	AC6	SOFTWARE	BU3 A:201 , HOH A:317 , HOH A:334	BINDING SITE FOR RESIDUE CL A 606
07	AC7	SOFTWARE	SER A:-1 , ASP A:112 , PRO A:113 , TYR A:127 , BU3 A:201	BINDING SITE FOR RESIDUE NA A 701
08	AC8	SOFTWARE	SER A:-1 , ASP A:112 , PRO A:113 , PRO A:115 , ASP A:116 , HOH A:319 , HOH A:353 , CL A:606 , NA A:701	BINDING SITE FOR RESIDUE BU3 A 201
09	AC9	SOFTWARE	ARG A:15 , HOH A:383 , HOH A:404	BINDING SITE FOR RESIDUE BU3 A 202
10	BC1	SOFTWARE	ASP A:28 , ASP A:29 , LEU A:30 , PHE A:31 , ARG A:139	BINDING SITE FOR RESIDUE UNX A 501
11	BC2	SOFTWARE	CL A:601	BINDING SITE FOR RESIDUE UNX A 502
12	BC3	SOFTWARE	ASP A:130	BINDING SITE FOR RESIDUE UNX A 503
13	BC4	SOFTWARE	SER A:22 , THR A:36	BINDING SITE FOR RESIDUE UNX A 504
14	BC5	SOFTWARE	LEU A:86 , ASN A:114 , HOH A:364	BINDING SITE FOR RESIDUE UNX A 505
15	BC6	SOFTWARE	VAL A:26 , ASP A:29 , SER A:94 , ARG A:139 , UNX A:508 , UNX A:509	BINDING SITE FOR RESIDUE UNX A 506
16	BC7	SOFTWARE	GLN A:34 , ALA A:35 , THR A:36	BINDING SITE FOR RESIDUE UNX A 507
17	BC8	SOFTWARE	GLY A:27 , ASP A:28 , ALA A:96 , ARG A:139 , UNX A:506	BINDING SITE FOR RESIDUE UNX A 508
18	BC9	SOFTWARE	HIS A:32 , SER A:94 , UNX A:506 , UNX A:510	BINDING SITE FOR RESIDUE UNX A 509
19	CC1	SOFTWARE	GLN A:136 , UNX A:509	BINDING SITE FOR RESIDUE UNX A 510

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:150
 aligned with UBC2_CAEEL | P35129 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:150
                               1                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147
           UBC2_CAEEL     - ---MALKRIQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPESPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRERYNQLAREWTQKYAM 147
               SCOP domains ---d1z2ua1 A:1-147 Ubiquitin conjugating enzyme, UBC                                                                                                   SCOP domains
               CATH domains 1z2uA00 A:-2-147 Ubiquitin Conjugating Enzyme                                                                                                          CATH domains
               Pfam domains -------UQ_con-1z2uA01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------Y------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z2u A  -2 GSHMALKRIQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPESPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRERYNQLAREWTQKYAM 147
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UBC2_CAEEL | P35129)

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: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: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: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.

Visualization

Interactive Views

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
		BU3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:60 - Pro A:61	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1z2u
		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
	UBC2_CAEEL \| P35129
		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

Analysis Tools

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
	UBC2_CAEEL \| P35129
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description