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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TUT1 BOUND WITH MGATP, FORM II
 
Authors :  S. Yamashita, K. Tomita
Date :  16 Dec 16  (Deposition) - 31 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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: SEQUENCE OF 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. C372A, C415A, 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

  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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:204 , SER A:205 , ASP A:216 , ASP A:218 , ASN A:392 , SER A:430 , TYR A:432 , HIS A:549 , MG A:1002 , HOH A:1101binding site for residue ATP A 1001
2AC2SOFTWARESER A:205 , ASP A:216 , ASP A:218 , ATP A:1001binding site for residue MG A 1002
3AC3SOFTWARETRP A:505binding site for residue CL A 1003
4AC4SOFTWARESER B:205 , ASP B:216 , ASP B:218 , ALA B:389 , ASN B:392 , SER B:393 , TYR B:432 , HIS B:549 , VAL B:551 , MG B:1002 , HOH B:1101binding site for residue ATP B 1001
5AC5SOFTWARESER B:205 , ASP B:216 , ASP B:218 , ATP B:1001binding site for residue MG B 1002
6AC6SOFTWARETRP B:505binding site for residue CL B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5WU4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:523 -Gly A:524
2Ala A:839 -Asp A:840
3Ala B:523 -Gly B:524
4Ala B:839 -Asp B:840

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5WU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5WU4)

(-) Exons   (0, 0)

(no "Exon" information available for 5WU4)

(-) 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 ..hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhh.........eeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.................hhhhhhhhhhhhhhhh....eeee....eeee...hhhhhhh........eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhhhhh..hhhhhhhhhh......eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu4 A 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLETPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFAHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRAWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKEGGWLATEAQVTQELKTEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLEH 877
                                   154       164       174       184       194       204       214       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       763       773       783       802       812  ||   832       842       852       862       872     
                                                                                                        223|                                                                                                                                                                                                                                                                                                                  637|                          792|          815|                                                   
                                                                                                         328                                                                                                                                                                                                                                                                                                                   763                           802           826                                                   


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...eeeeehhhh.........eeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhh......ee..ee.................hhhhhhhhhhhhhhhh....eeee....eeee....hhhhh.........eee.............hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh..hhhhhhhhh.ee....hhhhhhhhhhhhhhh....eee..eeeeeee......hhhhhhhhhhhhh...hhhhhhhhhh......eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wu4 B 145 DSHQLAKALAEAADVGAQMIKLVGLRELSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLETPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFAHRPSGLHGDVSLSNRLALHNSRFLSLCSELDGRVRPLVYTLRAWAQGRGLSGSGPLLSNYALTLLVIYFLQTRDPPVLPTVSQLTQKAGEGEQVEVDGWDCSFPRDASRLEPSINVEPLSSLLAQFFSAVSSWDLRGSLLSLREGQALPVAGGLPSNLWEGLRLGPLNLQDPFDLSHNVAANVTSRVAGRLQNCCRAAANYCRSLQYQRRSSRGRDWGLLPLLQPSSPSSLLSATPIPLPLAPFTQLTAALVQVFREALGCHIEQSASWRCALWHRVWQGRRRARRRLQQQTKGWLATEAQVTQELKTEPLLSFVASVSPADRMLTVTPLQDPQGLFPDLHHFLQVFLPQAIRHLKLEH 877
                                   154       164       174       184       194       204       214       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       763       773       783      |804       814||     834       844       854       864       874   
                                                                                                        223|                                                                                                                                                                                                                                                                                                                  637|                        790|          815|                                                   
                                                                                                         328                                                                                                                                                                                                                                                                                                                   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 5WU4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5WU4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5WU4)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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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 5wu5 5wu6

(-) Related Entries Specified in the PDB File

5wu1 5wu2 5wu3 5wu5 5wu6