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(-) Description

Title :  MINOR EDITOSOME-ASSOCIATED TUTASE 1 WITH BOUND UTP
 
Authors :  J. Stagno, H. Luecke
Date :  20 May 09  (Deposition) - 12 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tutase, Nucleotidyltransferase, Trypanosoma, Editosome, Rna Editing, Utp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Stagno, I. Aphasizheva, J. Bruystens, H. Luecke, R. Aphasizhev
Structure Of The Mitochondrial Editosome-Like Complex Associated Tutase 1 Reveals Divergent Mechanisms Of Utp Selection And Domain Organization.
J. Mol. Biol. V. 399 464 2010
PubMed-ID: 20403364  |  Reference-DOI: 10.1016/J.JMB.2010.04.021

(-) Compounds

Molecule 1 - MINOR EDITOSOME-ASSOCIATED TUTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TB927.1.1330
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:52 , GLY A:53 , SER A:54 , ASP A:65 , ASP A:67 , GLY A:138 , ASN A:141 , SER A:142 , LYS A:164 , LYS A:168 , ASN A:181 , SER A:182 , PHE A:183 , ASP A:335 , CYS A:342 , ARG A:345 , HOH A:415 , HOH A:423 , HOH A:434 , HOH A:494 , HOH A:584 , HOH A:645 , HOH A:648 , HOH A:650BINDING SITE FOR RESIDUE UTP A 501
2AC2SOFTWAREPHE B:52 , GLY B:53 , SER B:54 , ASP B:65 , ASP B:67 , GLY B:138 , ASN B:141 , SER B:142 , LYS B:164 , LYS B:168 , ASN B:181 , SER B:182 , PHE B:183 , ASP B:335 , CYS B:342 , ARG B:345 , HOH B:447 , HOH B:462 , HOH B:479 , HOH B:480 , HOH B:549 , HOH B:605 , HOH B:614 , HOH B:629 , HOH B:645BINDING SITE FOR RESIDUE UTP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HJ1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:307 -Pro A:308
2Gly B:307 -Pro B:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3HJ1)

(-) 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:384
 aligned with Q4GZ86_TRYB2 | Q4GZ86 from UniProtKB/TrEMBL  Length:406

    Alignment length:384
                              1                                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    
         Q4GZ86_TRYB2     - --MNVAKREFIRGMMAHYRASLPPPEHSVVIHELQKRVLDIGMLAVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKRMTRFGKEASAMGMEDVRYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLVKAWGKAREVIAPERSTFNSFTVTTMALMVLQELGLLPVFSKPTGEFGELTVADAEMLLQEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYAKYDFSAGTVSLIHPRRHRTVYERVVRRHLELLGSRKRLEWEKHIAEHKEDGPLDENDFSASMQNETTQRPSNSPYVVEDFVNYVNCGRRVQASRVRHIQQEFNRLREMLIDKESELKFDEVFRESD 382
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hj1 A  -1 GHMNVAKREFIRGMMAHYRASLPPPEHSVVIHELQKRVLDIGMLAVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKRMTRFGKEASAMGMEDVRYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLVKAWGKAREVIAPERSTFNSFTVTTMALMVLQELGLLPVFSKPTGEFGELTVADAEMLLQEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYAKYDFSAGTVSLIHPRRHRTVYERVVRRHLELLGSRKRLEWEKHIAEHKEDGPLDENDFSASMQNETTQRPSNSPYVVEDFVNYVNCGRRVQASRVRHIQQEFNRLREMLIDKESELKFDEVFRESD 382
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    


Chain B from PDB  Type:PROTEIN  Length:387
 aligned with Q4GZ86_TRYB2 | Q4GZ86 from UniProtKB/TrEMBL  Length:406

    Alignment length:387
                              1                                                                                                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       
         Q4GZ86_TRYB2     - --MNVAKREFIRGMMAHYRASLPPPEHSVVIHELQKRVLDIGMLAVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKRMTRFGKEASAMGMEDVRYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLVKAWGKAREVIAPERSTFNSFTVTTMALMVLQELGLLPVFSKPTGEFGELTVADAEMLLQEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYAKYDFSAGTVSLIHPRRHRTVYERVVRRHLELLGSRKRLEWEKHIAEHKEDGPLDENDFSASMQNETTQRPSNSPYVVEDFVNYVNCGRRVQASRVRHIQQEFNRLREMLIDKESELKFDEVFRESDTVP 385
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee..........hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hj1 B  -1 GHMNVAKREFIRGMMAHYRASLPPPEHSVVIHELQKRVLDIGMLAVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKRMTRFGKEASAMGMEDVRYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLVKAWGKAREVIAPERSTFNSFTVTTMALMVLQELGLLPVFSKPTGEFGELTVADAEMLLQEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYAKYDFSAGTVSLIHPRRHRTVYERVVRRHLELLGSRKRLEWEKHIAEHKEDGPLDENDFSASMQNETTQRPSNSPYVVEDFVNYVNCGRRVQASRVRHIQQEFNRLREMLIDKESELKFDEVFRESDTVP 385
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
   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 3HJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HJ1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4GZ86_TRYB2 | Q4GZ86)
molecular function
    GO:0050265    RNA uridylyltransferase activity    Catalysis of the reaction: UTP + RNA(n) = diphosphate + RNA(n+1).
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/TrEMBL
        Q4GZ86_TRYB2 | Q4GZ86: 3hiy 3hj4

(-) Related Entries Specified in the PDB File

3hiy MINOR EDITOSOME-ASSOCIATED TUTASE 1 WITH BOUND UTP AND MG
3hj4 MINOR EDITOSOME-ASSOCIATED TUTASE 1