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

(-) Description

Title :  CRYSTAL STRUCTURE OF S. CEREVISIAE SUMO E3 LIGASE SIZ1
 
Authors :  C. D. Lima, A. A. Yunus
Date :  29 Jun 09  (Deposition) - 15 Sep 09  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Sumo, Signal Transduction, Replication, Ring E3, Pias, Siz, Ubiquitin, Ubc9, Ligase, Metal-Binding, Nucleus, Phosphoprotein, Ubl Conjugation Pathway, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. A. Yunus, C. D. Lima
Structure Of The Siz/Pias Sumo E3 Ligase Siz1 And Determinants Required For Sumo Modification Of Pcna.
Mol. Cell V. 35 669 2009
PubMed-ID: 19748360  |  Reference-DOI: 10.1016/J.MOLCEL.2009.07.013

(-) Compounds

Molecule 1 - E3 SUMO-PROTEIN LIGASE SIZ1
    ChainsA
    EC Number6.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSMT3
    Expression System StrainBL21 (DE3) CP-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 112-465
    GeneSIZ1, ULL1, YDR409W
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainW3031A
    SynonymSAP AND MIZ-FINGER DOMAIN-CONTAINING PROTEIN 1, UBIQUITIN- LIKE PROTEIN LIGASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:377 , HIS A:379 , CYS A:400 , CYS A:403BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:250 -Pro A:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I2D)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PINITPS51466 PINIT domain profile.SIZ1_YEAST162-314  1A:162-314
2ZF_SP_RINGPS51044 Zinc finger SP-RING-type profile.SIZ1_YEAST346-423  1A:346-423

(-) Exons   (0, 0)

(no "Exon" information available for 3I2D)

(-) 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:280
 aligned with SIZ1_YEAST | Q04195 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:286
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438      
           SIZ1_YEAST   159 TNPDASSSSSSFAVPTIHFKESPFYKIQRLIPELVMNVEVTGGRGMCSAKFKLSKADYNLLSNPNSKHRLYLFSGMINPLGSRGNEPIQFPFPNELRCNNVQIKDNIRGFKSKPGTAKPADLTPHLKPYTQQNNVELIYAFTTKEYKLFGYIVEMITPEQLLEKVLQHPKIIKQATLLYLKKTLREDEEMGLTTTSTIMSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDILQNCQKNVEQVELTSDGKWTAIL 444
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhh....eeeeeeeee.....hhhhh.......eeeee..ee...........hhhhh.ee.hhhh......eeeeeeeeee...eeeeeeeeee.hhhhhhhhhhh....hhhhhhhhhhhhhhh..------.eeeee............eeee........eehhhhhhhhhhh............hhh.eeehhhhhhhhh.......eeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PINIT  PDB: A:162-314 UniProt: 162-314                                                                                                                   -------------------------------ZF_SP_RING  PDB: A:346-423 UniProt: 346-423                                   --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i2d A 159 TNPDASSSSSSFAVPTIHFKESPFYKIQRLIPELVMNVEVTGGRGMCSAKFKLSKADYNLLSNPNSKHRLYLFSGMINPLGSRGNEPIQFPFPNELRCNNVQIKDNIRGFKSKPGTAKPADLTPHLKPYTQQNNVELIYAFTTKEYKLFGYIVEMITPEQLLEKVLQHPKIIKQATLLYLKKTLREDE------TSTIMSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDILQNCQKNVEQVELTSDGKWTAIL 444
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       | -    |  358       368       378       388       398       408       418       428       438      
                                                                                                                                                                                                                     346    353                                                                                           

   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 3I2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I2D)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SIZ1_YEAST | Q04195)
molecular function
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0005940    septin ring    A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:250 - Pro A:251   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3i2d
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SIZ1_YEAST | Q04195
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.-.-.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SIZ1_YEAST | Q04195
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SIZ1_YEAST | Q041952rnn 5jne

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3I2D)