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(-) Description

Title :  A RETROVIRAL PROTEASE-LIKE DOMAIN IN THE EUKARYOTIC PROTEIN DDI1
 
Authors :  D. Fass, R. Sirkis
Date :  14 Aug 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Acid Protease Fold, Dimer, Retroviral Protease Domain, Protein Turnover (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sirkis, J. E. Gerst, D. Fass
Ddi1, A Eukaryotic Protein With The Retroviral Protease Fold.
J. Mol. Biol. V. 364 376 2006
PubMed-ID: 17010377  |  Reference-DOI: 10.1016/J.JMB.2006.08.086
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA DAMAGE-INDUCIBLE PROTEIN DDI1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAED4, PET3 DERIVATIVE
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RETROVIRAL PROTEASE-LIKE DOMAIN, RESIDUES 180- 325
    Gene: DDI1, VSM1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: V-SNARE-MASTER 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2I1A)

(-) Sites  (0, 0)

(no "Site" information available for 2I1A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I1A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I1A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I1A)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER143W1YER143W.1V:456314-4576001287DDI1_YEAST1-4284284A:200-324 (gaps)
B:199-325 (gaps)
C:199-325 (gaps)
D:201-323 (gaps)		125
127
127
123

(-) Sequences/Alignments

Asymmetric 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:114
 aligned with DDI1_YEAST | P40087 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:125
                                   209       219       229       239       249       259       269       279       289       299       309       319     
           DDI1_YEAST   200 QVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIP 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeee.......eeehhhhhhhhhhhhh....-----------..eeeeeeeeee..eeeeeeeeee.....eeehhhhhhhh..eee....eeee..eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:200-324 (gaps) UniProt: 1-428 [INCOMPLETE]                                                                   Transcript 1
                 2i1a A 200 QVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRF-----------IIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIP 324
                                   209       219       229       239      |  -       259       269       279       289       299       309       319     
                                                                        246         258                                                                  


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with DDI1_YEAST | P40087 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:127
                                   208       218       228       238       248       258       268       278       288       298       308       318       
           DDI1_YEAST   199 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPK 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeee......eeehhhhhhhhhhhh...------------...eeeeeeeeee..eeeeeeeeee.....eeeehhhhhhh..eee....eeee..eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:199-325 (gaps) UniProt: 1-428 [INCOMPLETE]                                                                     Transcript 1
                 2i1a B 199 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDK------------KIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPK 325
                                   208       218       228       238     |   -       258       268       278       288       298       308       318       
                                                                       244          257                                                                    


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with DDI1_YEAST | P40087 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:127
                                   208       218       228       238       248       258       268       278       288       298       308       318       
           DDI1_YEAST   199 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPK 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeee......eeehhhhhhh.hhhhh.---------------..eeeeeeeee..eeeeeeeeee.....eeeehhhhhhh..eee....eeee..eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:199-325 (gaps) UniProt: 1-428 [INCOMPLETE]                                                                     Transcript 1
                 2i1a C 199 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMID---------------IGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPK 325
                                   208       218       228       238    |    -         -|      268       278       288       298       308       318       
                                                                      243             259                                                                  


Chain D from PDB  Type:PROTEIN  Length:113
 aligned with DDI1_YEAST | P40087 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:123
                                   210       220       230       240       250       260       270       280       290       300       310       320   
           DDI1_YEAST   201 VPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEI 323
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee.......eeehhhhhhh.hhhhh...----------..eeeeeeeeeeee..eeeeeeeeee.....eeehhhhhhhh..eee....eeee..eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:201-323 (gaps) UniProt: 1-428 [INCOMPLETE]                                                                 Transcript 1
                 2i1a D 201 VPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKR----------GKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEI 323
                                   210       220       230       240    |    -     | 260       270       280       290       300       310       320   
                                                                      245        256
   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 2I1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I1A)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DDI1_YEAST | P40087)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDI1_YEAST | P40087: 2mr9 2mro 2mrp 2mws 2n7e 4z2z 5kes

(-) Related Entries Specified in the PDB File

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