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(-) Description

Title :  CRYSTAL STRUCTURE OF APO HUMAN TUT1, FORM III
 
Authors :  S. Yamashita, K. Tomita
Date :  16 Dec 16  (Deposition) - 31 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Terminal Nucleotidyl Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, Y. Takagi, T. Nagaike, K. Tomita
Crystal Structures Of U6 Snrna-Specific Terminal Uridylyltransferase
Nat Commun V. 8 15788 2017
PubMed-ID: 28589955  |  Reference-DOI: 10.1038/NCOMMS15788

(-) Compounds

Molecule 1 - SPECKLE TARGETED PIP5K1A-REGULATED POLY(A) POLYMERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.19, 2.7.7.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 141-874
    Gene: TUT1, RBM21
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: 141-874(C-TERM) OF HUMAN TUT1 WAS CLONED TO PET22B VECTOR WITH NDEI AND XHOI SITES. RESIDUES OF 235-304 AND 651-750 WERE DELETED FOR CRYSTALLIZATION. C501A AND C504S MUTATIONS WERE INTRODUCED TO IMPROVE THE CRYSTALS.
    Synonym: STAR-PAP,RNA-BINDING MOTIF PROTEIN 21,RNA-BINDING PROTEIN 21,U6 SNRNA-SPECIFIC TERMINAL URIDYLYLTRANSFERASE 1,U6-TUTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5WU5)

(-) Sites  (0, 0)

(no "Site" information available for 5WU5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5WU5)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu A:817 -Ser A:818
2Ala A:839 -Asp A:840
3Ala B:839 -Asp B:840
4Ala C:839 -Asp C:840
5Ala D:839 -Asp D:840

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5WU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5WU5)

(-) Exons   (0, 0)

(no "Exon" information available for 5WU5)

(-) 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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhh.........eeeeee..hhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh....eeee....eeee..................eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.............eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu5 A 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRCWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKEGGWLATEAQVTQELKGLSGGEERPETEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLE 876
                                   154       164       174       184       194       204       214       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637|      772       782       792|      811       821       831       841       851       861       871     
                                                                                                        223|                                                                                                                                                                                                                                                                                                         637|                          792|                                                                          
                                                                                                         337                                                                                                                                                                                                                                                                                                          763                           802                                                                          


Chain B from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.............eeeeee..hhhhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.................hhhhhhhhhhhhhhhh....eeee....eeee..................eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhh............eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu5 B 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRCWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKEGGWLATEAQVTQELKGEERPETEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLE 876
                                   154       164       174       184       194       204       214       335       345       355       365       375       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 ||    770       780       790 ||    809      |823       833       843       853       863       873   
                                                                                                        223|                                                                                                                                                                                                                                                                                                           637|                          792|           816|                                                       
                                                                                                         335                                                                                                                                                                                                                                                                                                            763                           802            821                                                       


Chain C from PDB  Type:PROTEIN  Length:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhh..........eeeee.....hhhhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.................hhhhhhhhhhhhhhhh....eeee....eeee....hhhhh.........eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhh...........eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu5 C 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDLAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRCWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKEGGWLATEAQVTQELKGERPETEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLE 876
                                   154       164       174       184       194       204       214       224 ||    342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632    || 767       777       787    || 806       816|      831       841       851       861       871     
                                                                                                           226|                                                                                                                                                                                                                                                                                                           637|                          792|           816|                                                      
                                                                                                            335                                                                                                                                                                                                                                                                                                            763                           802            822                                                      


Chain D from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee..............eeeee....hhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh....eeee....eeee..................eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhh......eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu5 D 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRCWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKEGGWLATEAQVTQELKTEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLE 876
                                   154       164       174       184       194       204       214       224||     339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       764       774       784       803       813 ||    833       843       853       863       873   
                                                                                                          225|                                                                                                                                                                                                                                                                                                               637|                          792|          815|                                                  
                                                                                                           331                                                                                                                                                                                                                                                                                                                763                           802           826
   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 5WU5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5WU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5WU5)

(-) Gene Ontology  (22, 22)

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  Cis Peptide Bonds
    Ala A:839 - Asp A:840   [ RasMol ]  
    Ala B:839 - Asp B:840   [ RasMol ]  
    Ala C:839 - Asp C:840   [ RasMol ]  
    Ala D:839 - Asp D:840   [ RasMol ]  
    Leu A:817 - Ser A:818   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        STPAP_HUMAN | Q9H6E5: 2e5g 5wu1 5wu2 5wu3 5wu4 5wu6

(-) Related Entries Specified in the PDB File

5wu1 5wu2 5wu3 5wu4 5wu6