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(-) Description

Title :  X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF PAT1 (DECAPPING ACTIVATOR)
 
Authors :  Z. Fourati-Kammoun, O. Kolesnikova, R. Back, J. Keller, N. Lazar, C. Ga Plesse, B. Seraphin, M. Graille
Date :  21 Jan 14  (Deposition) - 08 Oct 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Arm-Repeat Fold, Dcp2, Lsm1-7, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Fourati, O. Kolesnikova, R. Back, J. Keller, C. Charenton, V. Taverniti, C. G. Plesse, N. Lazar, D. Durand, H. Van Tilbeurgh, B. Seraphin, M. Graille
The C-Terminal Domain From S. Cerevisiae Pat1 Displays Two Conserved Regions Involved In Decapping Factor Recruitment.
Plos One V. 9 96828 2014
PubMed-ID: 24830408  |  Reference-DOI: 10.1371/JOURNAL.PONE.0096828

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1
    Chains: C, A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 473-796
    Gene: PAT1, MRT1, YCR077C, YCR77C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DECAPPING ACTIVATOR AND TRANSLATIONAL REPRESSOR PAT1, TOPOISOMERASE II-ASSOCIATED PROTEIN PAT1, MRNA TURNOVER PROTEIN 1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x):   C
Biological Unit 2 (1x): A  
Biological Unit 3 (1x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:674 , HOH C:1001 , HOH C:1105 , HOH C:1121BINDING SITE FOR RESIDUE MG C 901
2AC2SOFTWAREPHE C:529 , GLN C:563BINDING SITE FOR RESIDUE EDO C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OJJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:651 -Asn A:652

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OJJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OJJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4OJJ)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.........hhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ojj A 474 GKKFILELIETVYEEILDLEANLRNGQQTDSTAMWEALHIDDSSYDVNPFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALIKQDSSRSNILSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQNDKFMDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVY 787
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783    


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ojj B 480 ELIETVYEEIFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALIKQDSSRSNILSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVYRDGEISEL 795
                                   489|      532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692 ||    707       717       727       737       747       757       767       777       787        
                                   489|                                                                                                                                                                        694|                                                                                               
                                    523                                                                                                                                                                         700                                                                                               


Chain C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ojj C 476 KFILELIETVYEEILDLEANLRNGQQTDSTAMWEALHIDDSSYDVNPFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALIKQDSSRSNILSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQNDKFMDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVYRDGEISELKHH 798
                                   485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795
   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 4OJJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OJJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OJJ)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  4ojj
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  PAT1_YEAST | P25644
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAT1_YEAST | P25644: 4brw 4c8q 4n0a 4ogp

(-) Related Entries Specified in the PDB File

4ogp