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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 :  16 Jan 14  (Deposition) - 08 Oct 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Arm-Repeat Fold, Dcp2, Lsm1-7, Rna Binding Protein (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: 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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:742 , LYS A:769 , TYR A:773 , GLN A:774 , HOH A:1055 , LYS B:531BINDING SITE FOR RESIDUE MES A 901
2AC2SOFTWAREGLN A:774 , ASN A:777 , LEU A:778 , HOH A:1067 , TYR B:486 , LYS B:531 , ARG B:538BINDING SITE FOR RESIDUE EDO A 902
3AC3SOFTWARELYS A:575 , PRO A:576 , THR A:577 , HIS A:689 , HOH A:1009BINDING SITE FOR RESIDUE EDO A 903
4AC4SOFTWARELYS A:531 , GLN B:742 , LYS B:769 , TYR B:773 , GLN B:774 , EDO B:902 , HOH B:1066BINDING SITE FOR RESIDUE MES B 901
5AC5SOFTWARETYR A:486 , LYS A:531 , GLN B:774 , ASN B:777 , MES B:901 , HOH B:1061BINDING SITE FOR RESIDUE EDO B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:498 -Gly B:499

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGP)

(-) 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 hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogp A 474 GKKFILELIETVYEEILDLEANLRNGQQTDSTAMWEALHIDDSSYDVNPFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALILSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQNDKFMDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVYRDGEISELK 796
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643||     662       672       682       692       702       712       722       732       742       752       762       772       782       792    
                                                                                                                                                                                                    644|                                                                                                                                              
                                                                                                                                                                                                     654                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogp B 473 GGKKFILELIETVYEEILDLEANLRNGQQTDSTAMWEALHIDDSSYDVNPFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALIKQDSLSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQNDKFMDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVYRDGEISELK 796
                                   482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642     ||657       667       677       687       697       707       717       727       737       747       757       767       777       787         
                                                                                                                                                                                                         648|                                                                                                                                              
                                                                                                                                                                                                          654
   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 4OGP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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    Asn B:498 - Gly B:499   [ RasMol ]  
 
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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 4ojj

(-) Related Entries Specified in the PDB File

4ojj