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(-) Description

Title :  TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND UTP AND UMP
 
Authors :  J. Stagno, H. Luecke
Date :  21 May 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tutase, Trypanosoma, Nucleotidyltransferase, Utp-Binding, Rna-Editing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Stagno, I. Aphasizheva, R. Aphasizhev, H. Luecke
Dual Role Of The Rna Substrate In Selectivity And Catalysis By Terminal Uridylyl Transferases.
Proc. Natl. Acad. Sci. Usa V. 104 14634 2007
PubMed-ID: 17785418  |  Reference-DOI: 10.1073/PNAS.0704259104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA URIDYLYL TRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TUT4
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: RNA URIDYLYLTRANSFERASE 4

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UTP-1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:66 , ASP A:68 , UTP A:501 , HOH A:503 , HOH A:574BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREUTP A:501 , U5P A:502 , HOH A:503 , HOH A:504 , HOH A:603 , HOH A:604BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREPHE A:52 , GLY A:53 , 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:401 , MG A:402 , U5P A:502 , HOH A:503 , HOH A:504 , HOH A:516 , HOH A:535 , HOH A:574 , HOH A:578 , HOH A:580 , HOH A:604BINDING SITE FOR RESIDUE UTP A 501
4AC4SOFTWAREPHE A:52 , ASP A:68 , ARG A:121 , VAL A:122 , ARG A:126 , ASP A:136 , MG A:402 , UTP A:501 , HOH A:503 , HOH A:508 , HOH A:559 , HOH A:577 , HOH A:578 , HOH A:603 , HOH A:604BINDING SITE FOR RESIDUE U5P A 502
5AC5SOFTWAREGLY B:53 , SER B:54 , ASP B:68 , LEU B:151 , LYS B:173 , SER B:188 , ASN B:192 , HOH B:504 , HOH B:528 , HOH B:554 , HOH B:565BINDING SITE FOR RESIDUE U5P B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q0F)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q0F)

(-) 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:324
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:330
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....------.hhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee.....eeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....eeee......ee......hhhhhhhh............ee.............hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q0f A   3 PSPAVVGRSLVNSFKQFVS------HVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    12        |-     |  32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                             21     28                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:318
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:331
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh..--.eeeeehhhhhhh.......eeeeeehhhhhh...--------....hhhhhhhhhhhhhhhh...eeee..---..eeeee......eeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......hhhhh....................hhhhhhhhhhhhhhhhhh.....ee........ee.hhhh.hhhhhhhhhhh........................hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q0f B   3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVD--MRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGK--------AKGLQADILAKLARVIRQKHLSWNVEEVR---VPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
                                    12        22        32        42 |  |   52        62        72        |-       |92       102       112     | 122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 
                                                                    44 47                                81       90                         118 122
   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 2Q0F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q0F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q0F)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q381M1_TRYB2 | Q381M1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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
        Q381M1_TRYB2 | Q381M1: 2ikf 2nom 2q0c 2q0d 2q0e 2q0g 5kal

(-) Related Entries Specified in the PDB File

2ikf THE SAME PROTEIN WITH BOUND UTP SUBSTRATE.
2nom THE SAME PROTEIN WITH BOUND DUTP SUBSTRATE.
2q0c
2q0d
2q0e
2q0g