1TFF - JenaLib

Title :   STRUCTURE OF OTUBAIN-2

Authors :   M. H. Nanao, S. O. Tcherniuk, J. Chroboczek, O. Dideberg, A. Dessen, M. Y. Balakirev

Date :   27 May 04 (Deposition) - 03 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Nanao, S. O. Tcherniuk, J. Chroboczek, O. Dideberg, A. Dessen, M. Y. Balakirev
Crystal Structure Of Human Otubain 2.
Embo Rep. V. 5 783 2004
PubMed-ID: 15258613 | Reference-DOI: 10.1038/SJ.EMBOR.7400201
(for further references see the PDB file header)

Compounds

Molecule 1 - UBIQUITIN THIOLESTERASE PROTEIN OTUB2
	Chains	:	A
	EC Number	:	3.4.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	OTUBAIN-2
	Gene	:	OTUB2, OTB2, OTU2, C14ORF137
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	OTUBAIN 2, OTU DOMAIN-CONTAINING UBIQUITIN ALDEHYDE-BINDING PROTEIN 2, UBIQUITIN- SPECIFIC PROCESSING PROTEASE OTUB2, DEUBIQUITINATING ENZYME OTUB2

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (5, 5)

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000203664	1	ENSE00001011094	chr14:94492724-94492886	163	OTUB2_HUMAN	1-1	1	0	-	-
1.2	ENST00000203664	2	ENSE00000808725	chr14:94503726-94503821	96	OTUB2_HUMAN	2-33	32	1	A:7-33	27
1.3	ENST00000203664	3	ENSE00000659975	chr14:94505309-94505427	119	OTUB2_HUMAN	34-73	40	1	A:34-73	40
1.4	ENST00000203664	4	ENSE00000659976	chr14:94510317-94510401	85	OTUB2_HUMAN	73-101	29	1	A:73-101	29
1.5	ENST00000203664	5	ENSE00001174850	chr14:94510932-94511126	195	OTUB2_HUMAN	102-166	65	1	A:102-166	65
1.6	ENST00000203664	6	ENSE00001402552	chr14:94512062-94515276	3215	OTUB2_HUMAN	167-234	68	1	A:167-234 (gaps)	68

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:221
 aligned with OTUB2_HUMAN | Q96DC9 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:228
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226        
          OTUB2_HUMAN     7 NLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDGNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYAADKH 234
               SCOP domains d1tffa_ A: Ubiquitin thiolesterase protein OTUB2 (Otubain-2)                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Peptidase_C65-1tffA01 A:7-230                                                                                                                                                                                                   ---- Pfam domains
         Sec.struct. author .........hhhhhh.hhhhhhhhhhhhhhhheeeee......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhh..eeeee..-------...........eeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------OTU  PDB: A:40-231 UniProt: 40-231                                                                                                                                                              --- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:7-33      Exon 1.3  PDB: A:34-73 UniProt: 34-73   ----------------------------Exon 1.5  PDB: A:102-166 UniProt: 102-166                        Exon 1.6  PDB: A:167-234 (gaps) UniProt: 167-234                     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------Exon 1.4  PDB: A:73-101      ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1tff A   7 NLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEmDIKDFCTHEVEPmATECDHIQITALSQALSIALQVEYVD-------HHVFPEAATPSVYLLYKTSHYNILYAADKH 234
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156 |     166    |  176       186       196|      206       216       226        
                                                                                                                                                                                 158-MSE      171-MSE                   197     205

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 (0, 0)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OTUB2_HUMAN | Q96DC9)

molecular function
	GO:0019784	NEDD8-specific protease activity	Catalysis of the hydrolysis of NEDD8, a small ubiquitin-related modifier, from previously neddylated substrates.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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:0004843	thiol-dependent ubiquitin-specific protease activity	Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
	GO:0036459	thiol-dependent ubiquitinyl hydrolase activity	Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	GO:0035871	protein K11-linked deubiquitination	A protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein.
	GO:0071108	protein K48-linked deubiquitination	A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
	GO:0070536	protein K63-linked deubiquitination	A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
	GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1tff)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tff)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1tff
		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
	OTUB2_HUMAN \| Q96DC9
		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)
	3.4.-.-
		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

Description