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(-) Description

Title :  CRYSTAL STRUCTURE OF A PFU-PUL DOMAIN PAIR OF SACCHAROMYCES CEREVISIAE DOA1/UFD3
 
Authors :  H. Komori, R. Nishimasu, T. Kuno, Y. Higuchi
Date :  16 Dec 09  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  X
Keywords :  Armadillo-Like Repeat Structure, Nucleus, Ubl Conjugation Pathway, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nishimasu, H. Komori, Y. Higuchi, H. Nishimasu, H. Hiroaki
Crystal Structure Of A Pfu-Pul Domain Pair Of Saccharomyces Cerevisiae Doa1/Ufd3
Kobe J. Med. Sci. V. 56 E125 2010
PubMed-ID: 21063153

(-) Compounds

Molecule 1 - PROTEIN DOA1
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PFU-PUL DOMAIN, RESIDUES 354-715
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DOA1/UFD3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3L3F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L3F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu X:467 -Pro X:468

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L3F)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PULPS51396 PUL domain profile.DOA1_YEAST465-715  1X:465-715

(-) Exons   (0, 0)

(no "Exon" information available for 3L3F)

(-) 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 X from PDB  Type:PROTEIN  Length:316
 aligned with DOA1_YEAST | P36037 from UniProtKB/Swiss-Prot  Length:715

    Alignment length:340
                                   385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715
           DOA1_YEAST   376 KKIEFEGKTYDYVFDVDIEDGKPPLKLPINVSDNPYTAADNFLARYELPMSYRDQVVQFILKNTNGISLDQPNDNASSSAVSPSKTSVMKVLPVKQYLIMENYNPDTIFNGIVKINSNEKTFDDEILAQIGGALHDIDESWELLLSFANTIRSNWEIKTPAYDIVRLIVKKLPYSSDIKDYIEEGLGNKNITLTMLTVRILVNCFNNENWGVKLLESNQVYKSIFETIDTEFSQASAKQSQNLAIAVSTLIFNYSALVTKGNSDLELLPIVADAINTKYGPLEEYQECEEAAYRLTVAYGNLATVEPTLRQFANSVTWLANIKRSYGNVPRFKDIFDDLS 715
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PFU-3l3fX01 X:376-439                                           -------------------------PUL-3l3fX02 X:465-714                                                                                                                                                                                                                                     - Pfam domains
         Sec.struct. author ..eee..eee.eeeee........eeeee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh------------------------...............hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PUL  PDB: X:465-715 UniProt: 465-715                                                                                                                                                                                                                        PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l3f X 376 KKIEFEGKTYDYVFDVDIEDGKPPLKLPINVSDNPYTAADNFLARYELPmSYRDQVVQFILKNT------------------------mKVLPVKQYLImENYNPDTIFNGIVKINSNEKTFDDEILAQIGGALHDIDESWELLLSFANTIRSNWEIKTPAYDIVRLIVKKLPYSSDIKDYIEEGLGNKNITLTmLTVRILVNCFNNENWGVKLLESNQVYKSIFETIDTEFSQASAKQSQNLAIAVSTLIFNYSALVTKGNSDLELLPIVADAINTKYGPLEEYQECEEAAYRLTVAYGNLATVEPTLRQFANSVTWLANIKRSYGNVPRFKDIFDDLS 715
                                   385       395       405       415       425       435   |     -         -       465       475       485       495       505       515       525       535       545       555       565    |  575       585       595       605       615       625       635       645       655       665       675       685       695       705       715
                                                                           425-MSE       439                      464-MSE    475-MSE                                                                                        570-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 3L3F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L3F)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PFU] (5)
(-)
Clan: no clan defined [family: PUL] (1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (DOA1_YEAST | P36037)
molecular function
    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: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:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0010992    ubiquitin recycling    Any process involved in the maintenance of an internal steady state of ubiquitin monomers and free ubiquitin chains at the level of the cell by recycling ubiquitin from proteasome-bound ubiquitinated intermediates.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DOA1_YEAST | P36037: 3gae 3odt 3psp 3pst

(-) Related Entries Specified in the PDB File

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