Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE YEAST U-BOX-CONTAINING UBIQUITIN LIGASE UFD2P
 
Authors :  D. Tu, A. T. Brunger
Date :  06 Jul 07  (Deposition) - 18 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Helical Hairpin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tu, W. Li, Y. Ye, A. T. Brunger
Inaugural Article: Structure And Function Of The Yeast U-Box-Containing Ubiquitin Ligase Ufd2P.
Proc. Natl. Acad. Sci. Usa V. 104 15599 2007
PubMed-ID: 17890322  |  Reference-DOI: 10.1073/PNAS.0701369104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CONJUGATION FACTOR E4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UFD2
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: UBIQUITIN FUSION DEGRADATION PROTEIN 2, UB FUSION PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric/Biological Unit (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QJ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QJ0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:490 -Pro A:491
2Leu A:497 -Pro A:498
3Ser A:850 -Pro A:851

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QJ0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_BOXPS51698 U-box domain profile.UFD2_YEAST880-954  1A:880-951

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL190C1YDL190C.1IV:121593-1187082886UFD2_YEAST1-9619611A:1-951 (gaps)951

(-) 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:937
 aligned with UFD2_YEAST | P54860 from UniProtKB/Swiss-Prot  Length:961

    Alignment length:957
                                  1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       
           UFD2_YEAST     - ------MTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKLDKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAFINYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLLRSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKALKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQK 951
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhee.........ee...--------....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh.............hhhhhhh...............hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..........eee......eeehhhhhhhhh.................eehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------U_BOX  PDB: A:880-951 UniProt: 880-954                                   PROSITE
               Transcript 1 ------Exon 1.1  PDB: A:1-951 (gaps) UniProt: 1-961 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 2qj0 A  -5 GSEFRSmTAIEDILQITTDPSDTRGYSLLKS--------LGVDFIDTLLLYQLTENEKLDKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCmNGAFINYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLLRSKQQTAmIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDmISYFAHIANKNHLRRADHPPFKELSSNGFmSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKmGSEIKALKEEIEKVKKIAANHDVFARFITAQLSKmEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLYISKYQTSPIFRNPRLGSFVEFTTmVLRCPELVSNPHLKGKLVQLLSVGAmPLTDNSPGFmmDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQSQNNADFFVRFVARmLNDLTFLLDEGLSNLAEVHNIQNELD------------EDKELQTRLASASRQAKSSCGLADKSmKLFEIYSKDIPAAFVTPEIVYRLASmLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLmYTImKDPVILPASKmNIDRSTIKAHLLSDSTDPFNRmPLKLEDVTPNEELRQKILCFKKQK 951
                                  |  4        14        24|       34        44        54        64        74        84        94       104    |  114       124       134       144       154       164       174       184       194       204       214       224       234       244   |   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404  |    414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584     | 594     ||604       614       624       634       644       654       664       674     | 684       694       704 |       -    |  724       734       744|      754       764      |774       784       794       804       814       824       834       844       854       864       874       884     | 894       904|      914       924  |    934       944       
                                  1-MSE                  25       34                                                                        109-MSE                                                                                                                                    248-MSE                           282-MSE                       312-MSE                                                                                        407-MSE                            442-MSE                                                                                                                   564-MSE                   590-MSE   600-MSE                                                                         680-MSE                   706          719                       745-MSE                   771-MSE                                                                                                                890-MSE        905-MSE               927-MSE                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        601-MSE                                                                                                                                                                                                                                                                                              894-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2QJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QJ0)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UFD2_YEAST | P54860)
molecular function
    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: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.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
biological process
    GO:0071361    cellular response to ethanol    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 an ethanol stimulus.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

 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 2qj0)
 
  Cis Peptide Bonds
    Leu A:497 - Pro A:498   [ RasMol ]  
    Phe A:490 - Pro A:491   [ RasMol ]  
    Ser A:850 - Pro A:851   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qj0
    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
  UFD2_YEAST | P54860
    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)
  (no 'Enzyme Classificator' available)
    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
  UFD2_YEAST | P54860
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UFD2_YEAST | P54860: 2qiz 3m62 3m63

(-) Related Entries Specified in the PDB File

2qiz THE SAME PROTEIN IN A DIFFERENT CONFORMATION.