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(-) Description

Title :  TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND UTP AND UPU
 
Authors :  J. R. Stagno, H. Luecke, R. Afasizhev
Date :  01 Jun 16  (Deposition) - 26 Oct 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,Y,Z
Biol. Unit 1:  A,Y  (1x)
Biol. Unit 2:  B,Z  (1x)
Keywords :  Trypanosoma, Rna Editing, Tutase, Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Rajappa-Titu, T. Suematsu, P. Munoz-Tello, M. Long, O. Demir, K. J. Cheng, J. R. Stagno, H. Luecke, R. E. Amaro, I. Aphasizheva, R. Aphasizhev, S. Thore
Rna Editing Tutase 1: Structural Foundation Of Substrate Recognition, Complex Interactions And Drug Targeting.
Nucleic Acids Res. V. 44 10862 2016
PubMed-ID: 27744351  |  Reference-DOI: 10.1093/NAR/GKW917

(-) Compounds

Molecule 1 - RNA URIDYLYLTRANSFERASE 4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TUT4
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
 
Molecule 2 - RNA (5'-R(*UP*U)-3')
    Chains: Y, Z
    Engineered: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABYZ
Biological Unit 1 (1x): A Y 
Biological Unit 2 (1x):  B Z

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:52 , SER A:54 , SER A:65 , ASP A:66 , ASP A:68 , GLY A:144 , ASN A:147 , SER A:148 , LYS A:169 , LYS A:173 , SER A:188 , TYR A:189 , MG A:502 , HOH A:602 , HOH A:603 , HOH A:610 , HOH A:613 , HOH A:624 , HOH A:636 , HOH A:638 , U Y:2 , MG Y:101binding site for residue UTP A 501
2AC2SOFTWAREASP A:66 , ASP A:68 , UTP A:501 , HOH A:602 , HOH A:638binding site for residue MG A 502
3AC3SOFTWAREPHE B:52 , SER B:54 , SER B:65 , ASP B:66 , ASP B:68 , GLY B:144 , ASN B:147 , SER B:148 , LYS B:169 , LYS B:173 , SER B:188 , TYR B:189 , MG B:402 , HOH B:505 , HOH B:506 , HOH B:507 , HOH B:508 , HOH B:524 , HOH B:526 , U Z:2 , MG Z:101binding site for residue UTP B 401
4AC4SOFTWAREASP B:66 , ASP B:68 , UTP B:401 , HOH B:507 , HOH B:508 , MG Z:101binding site for residue MG B 402
5AC5SOFTWAREASP B:66 , ARG B:126 , ASP B:136binding site for residue MG B 403
6AC6SOFTWAREUTP A:501 , HOH A:602 , HOH A:610 , HOH A:613 , HOH A:649 , U Y:2 , HOH Y:205binding site for residue MG Y 101
7AC7SOFTWAREUTP B:401 , MG B:402 , HOH B:505 , HOH B:506 , HOH B:507 , HOH B:527 , U Z:2 , HOH Z:202binding site for residue MG Z 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KAL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KAL)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeeee...eeeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....ee........ee.hhhh.hhhhhhhh...........................hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kal A   2 PPSPAVVGRSLVNSFKQFVSHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    11        21|       37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
                                              21|                                                                                                                                                                                                                                                                                                                
                                               28                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee..eeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....ee........ee.hhhh.hhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kal B   2 PPSPAVVGRSLVNSFKVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    11     || 32        42        52        62        72        82        92       102       112       122      |136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326      
                                          17|                                                                                                 129|                                                                                                                                                                                                      
                                           29                                                                                                  134                                                                                                                                                                                                      


Chain Y from PDB  Type:RNA  Length:2
                                  
                 5kal Y   1 UU   2


Chain Z from PDB  Type:RNA  Length:2
                                  
                 5kal Z   1 UU   2
   Legend:   → Mismatch (orange background)
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  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 5KAL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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        Q381M1_TRYB2 | Q381M1: 2ikf 2nom 2q0c 2q0d 2q0e 2q0f 2q0g

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